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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "# Convert 3k PBMCs AnnData to Xarray" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "outputs": [], | |
| "source": [], | |
| "metadata": { | |
| "collapsed": false, | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| } | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "This assumes you have a single cell anndata plot file.\n", | |
| "\n", | |
| "If you go through this tutorial - https://github.com/scverse/scanpy-tutorials/blob/master/pbmc3k.ipynb you can use the `'write/pbmc3k.h5ad` you get at the end. \n", | |
| "\n", | |
| "The general idea is to convert the AnnData object to an XArray object, dump to zarr, and then read it back in. When you read it back in you will have a lazily loaded object with dask arrays instead of in memory arrays." | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "<div class=\"alert alert-info\">\n", | |
| "\n", | |
| "**Note**\n", | |
| "\n", | |
| "This assumes you have a single cell anndata plot file.\n", | |
| "\n", | |
| "If you go through this tutorial - [pbmc3k.ipynb](https://github.com/scverse/scanpy-tutorials/blob/master/pbmc3k.ipynb) you can use the `'write/pbmc3k.h5ad` you get at the end. \n", | |
| " \n", | |
| "Download the notebook by clicking on the _Edit on GitHub_ button. On GitHub, you can download using the _Raw_ button via right-click and _Save Link As_. Alternatively, download the whole [scanpy-tutorial](https://github.com/theislab/scanpy-tutorials) repository.\n", | |
| "</div> " | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "import numpy as np\n", | |
| "import pandas as pd\n", | |
| "import scanpy as sc\n", | |
| "import anndata\n", | |
| "import dask\n", | |
| "import dask.array as da\n", | |
| "import dask.dataframe as dd\n", | |
| "import glob\n", | |
| "import os\n", | |
| "import xarray as xr\n", | |
| "import zarr\n", | |
| "from typing import Union, Literal, Any, List\n", | |
| "from pathlib import Path\n", | |
| "import seaborn as sns\n", | |
| "\n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "/Users/jillian/opt/miniconda3/envs/scanpy/lib/python3.10/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", | |
| " from .autonotebook import tqdm as notebook_tqdm\n" | |
| ] | |
| }, | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "scanpy==1.7.2 anndata==0.8.0 umap==0.5.3 numpy==1.21.6 scipy==1.8.0 pandas==1.4.2 scikit-learn==1.1.0 statsmodels==0.13.2 python-igraph==0.9.10\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "sc.settings.verbosity = 3 # verbosity: errors (0), warnings (1), info (2), hints (3)\n", | |
| "sc.logging.print_header()\n", | |
| "sc.settings.set_figure_params(dpi=80, facecolor='white')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "You should have the results from the previous `pbmc3k.h5ad` stored to a h5ad file and a zarr file." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "results_file = 'write/pbmc3k.h5ad' # the file that will store the analysis results" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "AnnData object with n_obs × n_vars = 2638 × 1838\n", | |
| " obs: 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'leiden'\n", | |
| " var: 'gene_ids', 'n_cells', 'mt', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'\n", | |
| " uns: 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'rank_genes_groups', 'umap'\n", | |
| " obsm: 'X_pca', 'X_umap'\n", | |
| " varm: 'PCs'\n", | |
| " obsp: 'connectivities', 'distances'" | |
| ] | |
| }, | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata = anndata.read(results_file)\n", | |
| "adata" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "dict_keys(['logfoldchanges', 'names', 'params', 'pvals', 'pvals_adj', 'scores'])" | |
| ] | |
| }, | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "#help(adata)\n", | |
| "adata.uns['rank_genes_groups'].keys()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>CD4 T</th>\n", | |
| " <th>CD14 Monocytes</th>\n", | |
| " <th>B</th>\n", | |
| " <th>CD8 T</th>\n", | |
| " <th>NK</th>\n", | |
| " <th>FCGR3A Monocytes</th>\n", | |
| " <th>Dendritic</th>\n", | |
| " <th>Megakaryocytes</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>1.041539</td>\n", | |
| " <td>7.359957</td>\n", | |
| " <td>4.079535</td>\n", | |
| " <td>5.321771</td>\n", | |
| " <td>5.141453</td>\n", | |
| " <td>6.868872</td>\n", | |
| " <td>4.278315</td>\n", | |
| " <td>12.905741</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>2.668251</td>\n", | |
| " <td>6.166798</td>\n", | |
| " <td>7.749746</td>\n", | |
| " <td>4.925867</td>\n", | |
| " <td>4.886553</td>\n", | |
| " <td>7.695069</td>\n", | |
| " <td>4.434846</td>\n", | |
| " <td>11.863666</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>1.164884</td>\n", | |
| " <td>7.482893</td>\n", | |
| " <td>4.887034</td>\n", | |
| " <td>0.765132</td>\n", | |
| " <td>4.791256</td>\n", | |
| " <td>7.759242</td>\n", | |
| " <td>4.608550</td>\n", | |
| " <td>12.428451</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>1.017071</td>\n", | |
| " <td>5.334051</td>\n", | |
| " <td>5.518004</td>\n", | |
| " <td>4.195086</td>\n", | |
| " <td>3.645046</td>\n", | |
| " <td>4.807891</td>\n", | |
| " <td>4.237393</td>\n", | |
| " <td>13.035219</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>0.868595</td>\n", | |
| " <td>5.443555</td>\n", | |
| " <td>4.065814</td>\n", | |
| " <td>4.111341</td>\n", | |
| " <td>2.986083</td>\n", | |
| " <td>6.341140</td>\n", | |
| " <td>3.639149</td>\n", | |
| " <td>9.092909</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>...</th>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13709</th>\n", | |
| " <td>-3.791953</td>\n", | |
| " <td>-1.231050</td>\n", | |
| " <td>-4.344168</td>\n", | |
| " <td>-2.135163</td>\n", | |
| " <td>-0.946669</td>\n", | |
| " <td>-0.945360</td>\n", | |
| " <td>-0.607817</td>\n", | |
| " <td>-4.380812</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13710</th>\n", | |
| " <td>-4.612272</td>\n", | |
| " <td>-1.174195</td>\n", | |
| " <td>-3.686769</td>\n", | |
| " <td>-2.427655</td>\n", | |
| " <td>-1.061288</td>\n", | |
| " <td>-1.054185</td>\n", | |
| " <td>-1.225529</td>\n", | |
| " <td>-5.583522</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13711</th>\n", | |
| " <td>-4.363408</td>\n", | |
| " <td>-1.219507</td>\n", | |
| " <td>-3.159241</td>\n", | |
| " <td>-1.080934</td>\n", | |
| " <td>-0.972080</td>\n", | |
| " <td>-1.052498</td>\n", | |
| " <td>-0.793074</td>\n", | |
| " <td>-5.350221</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13712</th>\n", | |
| " <td>-2.075822</td>\n", | |
| " <td>-2.032438</td>\n", | |
| " <td>-0.862879</td>\n", | |
| " <td>-0.760947</td>\n", | |
| " <td>-1.012957</td>\n", | |
| " <td>-1.336820</td>\n", | |
| " <td>-0.772327</td>\n", | |
| " <td>-3.965278</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13713</th>\n", | |
| " <td>-2.818502</td>\n", | |
| " <td>-1.597620</td>\n", | |
| " <td>-3.911268</td>\n", | |
| " <td>-0.667920</td>\n", | |
| " <td>-1.201607</td>\n", | |
| " <td>-1.285712</td>\n", | |
| " <td>-1.179082</td>\n", | |
| " <td>-4.840257</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "<p>13714 rows × 8 columns</p>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " CD4 T CD14 Monocytes B CD8 T NK \\\n", | |
| "0 1.041539 7.359957 4.079535 5.321771 5.141453 \n", | |
| "1 2.668251 6.166798 7.749746 4.925867 4.886553 \n", | |
| "2 1.164884 7.482893 4.887034 0.765132 4.791256 \n", | |
| "3 1.017071 5.334051 5.518004 4.195086 3.645046 \n", | |
| "4 0.868595 5.443555 4.065814 4.111341 2.986083 \n", | |
| "... ... ... ... ... ... \n", | |
| "13709 -3.791953 -1.231050 -4.344168 -2.135163 -0.946669 \n", | |
| "13710 -4.612272 -1.174195 -3.686769 -2.427655 -1.061288 \n", | |
| "13711 -4.363408 -1.219507 -3.159241 -1.080934 -0.972080 \n", | |
| "13712 -2.075822 -2.032438 -0.862879 -0.760947 -1.012957 \n", | |
| "13713 -2.818502 -1.597620 -3.911268 -0.667920 -1.201607 \n", | |
| "\n", | |
| " FCGR3A Monocytes Dendritic Megakaryocytes \n", | |
| "0 6.868872 4.278315 12.905741 \n", | |
| "1 7.695069 4.434846 11.863666 \n", | |
| "2 7.759242 4.608550 12.428451 \n", | |
| "3 4.807891 4.237393 13.035219 \n", | |
| "4 6.341140 3.639149 9.092909 \n", | |
| "... ... ... ... \n", | |
| "13709 -0.945360 -0.607817 -4.380812 \n", | |
| "13710 -1.054185 -1.225529 -5.583522 \n", | |
| "13711 -1.052498 -0.793074 -5.350221 \n", | |
| "13712 -1.336820 -0.772327 -3.965278 \n", | |
| "13713 -1.285712 -1.179082 -4.840257 \n", | |
| "\n", | |
| "[13714 rows x 8 columns]" | |
| ] | |
| }, | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "pd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges'])" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Get the Dataframes\n", | |
| "\n", | |
| "Get the dataframes for the vars and obs" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
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| "\n", | |
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| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>n_genes</th>\n", | |
| " <th>n_genes_by_counts</th>\n", | |
| " <th>total_counts</th>\n", | |
| " <th>total_counts_mt</th>\n", | |
| " <th>pct_counts_mt</th>\n", | |
| " <th>leiden</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>AAACATACAACCAC-1</th>\n", | |
| " <td>781</td>\n", | |
| " <td>779</td>\n", | |
| " <td>2419.0</td>\n", | |
| " <td>73.0</td>\n", | |
| " <td>3.017776</td>\n", | |
| " <td>CD8 T</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>AAACATTGAGCTAC-1</th>\n", | |
| " <td>1352</td>\n", | |
| " <td>1352</td>\n", | |
| " <td>4903.0</td>\n", | |
| " <td>186.0</td>\n", | |
| " <td>3.793596</td>\n", | |
| " <td>B</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>AAACATTGATCAGC-1</th>\n", | |
| " <td>1131</td>\n", | |
| " <td>1129</td>\n", | |
| " <td>3147.0</td>\n", | |
| " <td>28.0</td>\n", | |
| " <td>0.889736</td>\n", | |
| " <td>CD4 T</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>AAACCGTGCTTCCG-1</th>\n", | |
| " <td>960</td>\n", | |
| " <td>960</td>\n", | |
| " <td>2639.0</td>\n", | |
| " <td>46.0</td>\n", | |
| " <td>1.743085</td>\n", | |
| " <td>NK</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>AAACCGTGTATGCG-1</th>\n", | |
| " <td>522</td>\n", | |
| " <td>521</td>\n", | |
| " <td>980.0</td>\n", | |
| " <td>12.0</td>\n", | |
| " <td>1.224490</td>\n", | |
| " <td>FCGR3A Monocytes</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " n_genes n_genes_by_counts total_counts total_counts_mt \\\n", | |
| "AAACATACAACCAC-1 781 779 2419.0 73.0 \n", | |
| "AAACATTGAGCTAC-1 1352 1352 4903.0 186.0 \n", | |
| "AAACATTGATCAGC-1 1131 1129 3147.0 28.0 \n", | |
| "AAACCGTGCTTCCG-1 960 960 2639.0 46.0 \n", | |
| "AAACCGTGTATGCG-1 522 521 980.0 12.0 \n", | |
| "\n", | |
| " pct_counts_mt leiden \n", | |
| "AAACATACAACCAC-1 3.017776 CD8 T \n", | |
| "AAACATTGAGCTAC-1 3.793596 B \n", | |
| "AAACATTGATCAGC-1 0.889736 CD4 T \n", | |
| "AAACCGTGCTTCCG-1 1.743085 NK \n", | |
| "AAACCGTGTATGCG-1 1.224490 FCGR3A Monocytes " | |
| ] | |
| }, | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata.obs.head()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>gene_ids</th>\n", | |
| " <th>n_cells</th>\n", | |
| " <th>mt</th>\n", | |
| " <th>n_cells_by_counts</th>\n", | |
| " <th>mean_counts</th>\n", | |
| " <th>pct_dropout_by_counts</th>\n", | |
| " <th>total_counts</th>\n", | |
| " <th>highly_variable</th>\n", | |
| " <th>means</th>\n", | |
| " <th>dispersions</th>\n", | |
| " <th>dispersions_norm</th>\n", | |
| " <th>mean</th>\n", | |
| " <th>std</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>TNFRSF4</th>\n", | |
| " <td>ENSG00000186827</td>\n", | |
| " <td>155</td>\n", | |
| " <td>False</td>\n", | |
| " <td>155</td>\n", | |
| " <td>0.077407</td>\n", | |
| " <td>94.259259</td>\n", | |
| " <td>209.0</td>\n", | |
| " <td>True</td>\n", | |
| " <td>0.277410</td>\n", | |
| " <td>2.086050</td>\n", | |
| " <td>0.665406</td>\n", | |
| " <td>-3.672069e-10</td>\n", | |
| " <td>0.424481</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>CPSF3L</th>\n", | |
| " <td>ENSG00000127054</td>\n", | |
| " <td>202</td>\n", | |
| " <td>False</td>\n", | |
| " <td>202</td>\n", | |
| " <td>0.094815</td>\n", | |
| " <td>92.518519</td>\n", | |
| " <td>256.0</td>\n", | |
| " <td>True</td>\n", | |
| " <td>0.385194</td>\n", | |
| " <td>4.506987</td>\n", | |
| " <td>2.955005</td>\n", | |
| " <td>-2.372437e-10</td>\n", | |
| " <td>0.460416</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>ATAD3C</th>\n", | |
| " <td>ENSG00000215915</td>\n", | |
| " <td>9</td>\n", | |
| " <td>False</td>\n", | |
| " <td>9</td>\n", | |
| " <td>0.009259</td>\n", | |
| " <td>99.666667</td>\n", | |
| " <td>25.0</td>\n", | |
| " <td>True</td>\n", | |
| " <td>0.038252</td>\n", | |
| " <td>3.953486</td>\n", | |
| " <td>4.352607</td>\n", | |
| " <td>8.472988e-12</td>\n", | |
| " <td>0.119465</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>C1orf86</th>\n", | |
| " <td>ENSG00000162585</td>\n", | |
| " <td>501</td>\n", | |
| " <td>False</td>\n", | |
| " <td>501</td>\n", | |
| " <td>0.227778</td>\n", | |
| " <td>81.444444</td>\n", | |
| " <td>615.0</td>\n", | |
| " <td>True</td>\n", | |
| " <td>0.678283</td>\n", | |
| " <td>2.713522</td>\n", | |
| " <td>0.543183</td>\n", | |
| " <td>3.389195e-10</td>\n", | |
| " <td>0.685145</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>RER1</th>\n", | |
| " <td>ENSG00000157916</td>\n", | |
| " <td>608</td>\n", | |
| " <td>False</td>\n", | |
| " <td>608</td>\n", | |
| " <td>0.298148</td>\n", | |
| " <td>77.481481</td>\n", | |
| " <td>805.0</td>\n", | |
| " <td>True</td>\n", | |
| " <td>0.814813</td>\n", | |
| " <td>3.447533</td>\n", | |
| " <td>1.582528</td>\n", | |
| " <td>7.696297e-11</td>\n", | |
| " <td>0.736050</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " gene_ids n_cells mt n_cells_by_counts mean_counts \\\n", | |
| "TNFRSF4 ENSG00000186827 155 False 155 0.077407 \n", | |
| "CPSF3L ENSG00000127054 202 False 202 0.094815 \n", | |
| "ATAD3C ENSG00000215915 9 False 9 0.009259 \n", | |
| "C1orf86 ENSG00000162585 501 False 501 0.227778 \n", | |
| "RER1 ENSG00000157916 608 False 608 0.298148 \n", | |
| "\n", | |
| " pct_dropout_by_counts total_counts highly_variable means \\\n", | |
| "TNFRSF4 94.259259 209.0 True 0.277410 \n", | |
| "CPSF3L 92.518519 256.0 True 0.385194 \n", | |
| "ATAD3C 99.666667 25.0 True 0.038252 \n", | |
| "C1orf86 81.444444 615.0 True 0.678283 \n", | |
| "RER1 77.481481 805.0 True 0.814813 \n", | |
| "\n", | |
| " dispersions dispersions_norm mean std \n", | |
| "TNFRSF4 2.086050 0.665406 -3.672069e-10 0.424481 \n", | |
| "CPSF3L 4.506987 2.955005 -2.372437e-10 0.460416 \n", | |
| "ATAD3C 3.953486 4.352607 8.472988e-12 0.119465 \n", | |
| "C1orf86 2.713522 0.543183 3.389195e-10 0.685145 \n", | |
| "RER1 3.447533 1.582528 7.696297e-11 0.736050 " | |
| ] | |
| }, | |
| "execution_count": 8, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata.var.head()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Create the XArray object\n", | |
| "\n", | |
| "XArray datasets can be created directly from dataframes.\n", | |
| "\n", | |
| "1. Create one xr dataset from the `var` dataframe and rename the index to `vars`.\n", | |
| "2. Create one xr datasets from the `obs` dataframe and rename the index to `obs`.\n", | |
| "3. Combine the datasets " | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 9, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "\n", | |
| "def get_anndata_attr(\n", | |
| " adata: anndata.AnnData,\n", | |
| " adata_ds: xr.Dataset,\n", | |
| " attr: str\n", | |
| ") -> xr.Dataset:\n", | |
| " try:\n", | |
| " adata_attr = getattr(adata, attr)\n", | |
| " for key in list(adata_attr.keys()):\n", | |
| " coords = {}\n", | |
| " for i in np.arange(len(adata_attr[key].shape)):\n", | |
| " coords[f'{key}_{i}'] = np.arange(adata_attr[key].shape[i])\n", | |
| " adata_ds.coords.update(coords)\n", | |
| " xr_da = xr.DataArray(\n", | |
| " coords=coords,\n", | |
| " dims=list(coords.keys()),\n", | |
| " data=da.from_array(adata_attr[key])\n", | |
| " )\n", | |
| " adata_ds[key] = xr_da\n", | |
| " except Exception as e:\n", | |
| " print(f'Unable to add: {attr} to dataset')\n", | |
| " return adata_ds\n", | |
| " return adata_ds\n", | |
| "\n", | |
| "\n", | |
| "def convert_anndata_to_xarray(anndata_file: Union[str, Path]) -> xr.Dataset:\n", | |
| " adata = anndata.read(anndata_file)\n", | |
| " adata_var = xr.Dataset.from_dataframe(adata.var).rename({'index': 'vars'})\n", | |
| " adata_obs = xr.Dataset.from_dataframe(adata.obs).rename({'index': 'obs'})\n", | |
| " adata_ds = xr.Dataset(coords={'obs': adata_obs.obs, 'vars': adata_var.vars})\n", | |
| "\n", | |
| " for key in list(adata_obs.data_vars.keys()):\n", | |
| " adata_ds[key] = adata_obs[key]\n", | |
| " for key in list(adata_var.data_vars.keys()):\n", | |
| " adata_ds[key] = adata_var[key]\n", | |
| "\n", | |
| " adata_ds = get_anndata_attr(adata=adata, adata_ds=adata_ds, attr='varm')\n", | |
| " adata_ds = get_anndata_attr(adata=adata, adata_ds=adata_ds, attr='obsm')\n", | |
| " #adata_ds = get_anndata_attr(adata=adata, adata_ds=adata_ds, attr='obsp')\n", | |
| "\n", | |
| " return adata_ds\n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 10, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
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| "<defs>\n", | |
| "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n", | |
| "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n", | |
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| "</symbol>\n", | |
| "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n", | |
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| "</symbol>\n", | |
| "</defs>\n", | |
| "</svg>\n", | |
| "<style>/* CSS stylesheet for displaying xarray objects in jupyterlab.\n", | |
| " *\n", | |
| " */\n", | |
| "\n", | |
| ":root {\n", | |
| " --xr-font-color0: var(--jp-content-font-color0, rgba(0, 0, 0, 1));\n", | |
| " --xr-font-color2: var(--jp-content-font-color2, rgba(0, 0, 0, 0.54));\n", | |
| " --xr-font-color3: var(--jp-content-font-color3, rgba(0, 0, 0, 0.38));\n", | |
| " --xr-border-color: var(--jp-border-color2, #e0e0e0);\n", | |
| " --xr-disabled-color: var(--jp-layout-color3, #bdbdbd);\n", | |
| " --xr-background-color: var(--jp-layout-color0, white);\n", | |
| " --xr-background-color-row-even: var(--jp-layout-color1, white);\n", | |
| " --xr-background-color-row-odd: var(--jp-layout-color2, #eeeeee);\n", | |
| "}\n", | |
| "\n", | |
| "html[theme=dark],\n", | |
| "body.vscode-dark {\n", | |
| " --xr-font-color0: rgba(255, 255, 255, 1);\n", | |
| " --xr-font-color2: rgba(255, 255, 255, 0.54);\n", | |
| " --xr-font-color3: rgba(255, 255, 255, 0.38);\n", | |
| " --xr-border-color: #1F1F1F;\n", | |
| " --xr-disabled-color: #515151;\n", | |
| " --xr-background-color: #111111;\n", | |
| " --xr-background-color-row-even: #111111;\n", | |
| " --xr-background-color-row-odd: #313131;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-wrap {\n", | |
| " display: block !important;\n", | |
| " min-width: 300px;\n", | |
| " max-width: 700px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-text-repr-fallback {\n", | |
| " /* fallback to plain text repr when CSS is not injected (untrusted notebook) */\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-header {\n", | |
| " padding-top: 6px;\n", | |
| " padding-bottom: 6px;\n", | |
| " margin-bottom: 4px;\n", | |
| " border-bottom: solid 1px var(--xr-border-color);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-header > div,\n", | |
| ".xr-header > ul {\n", | |
| " display: inline;\n", | |
| " margin-top: 0;\n", | |
| " margin-bottom: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-obj-type,\n", | |
| ".xr-array-name {\n", | |
| " margin-left: 2px;\n", | |
| " margin-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-obj-type {\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-sections {\n", | |
| " padding-left: 0 !important;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 150px auto auto 1fr 20px 20px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input + label {\n", | |
| " color: var(--xr-disabled-color);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input:enabled + label {\n", | |
| " cursor: pointer;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input:enabled + label:hover {\n", | |
| " color: var(--xr-font-color0);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary {\n", | |
| " grid-column: 1;\n", | |
| " color: var(--xr-font-color2);\n", | |
| " font-weight: 500;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary > span {\n", | |
| " display: inline-block;\n", | |
| " padding-left: 0.5em;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:disabled + label {\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in + label:before {\n", | |
| " display: inline-block;\n", | |
| " content: '►';\n", | |
| " font-size: 11px;\n", | |
| " width: 15px;\n", | |
| " text-align: center;\n", | |
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| ".xr-section-summary-in:disabled + label:before {\n", | |
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| ".xr-section-summary-in:checked + label:before {\n", | |
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| ".xr-section-summary-in:checked + label > span {\n", | |
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| " display: grid;\n", | |
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| "\n", | |
| ".xr-array-wrap > label {\n", | |
| " grid-column: 1;\n", | |
| " vertical-align: top;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-preview {\n", | |
| " color: var(--xr-font-color3);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-preview,\n", | |
| ".xr-array-data {\n", | |
| " padding: 0 5px !important;\n", | |
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| " display: inline-block !important;\n", | |
| " list-style: none;\n", | |
| " padding: 0 !important;\n", | |
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| "}\n", | |
| "\n", | |
| ".xr-dim-list li {\n", | |
| " display: inline-block;\n", | |
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| ".xr-dim-list:before {\n", | |
| " content: '(';\n", | |
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| ".xr-dim-list:after {\n", | |
| " content: ')';\n", | |
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| ".xr-var-item > .xr-var-name span {\n", | |
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| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
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| "}\n", | |
| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-odd);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name {\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
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| " grid-column: 3;\n", | |
| " text-align: right;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-preview {\n", | |
| " grid-column: 4;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name,\n", | |
| ".xr-var-dims,\n", | |
| ".xr-var-dtype,\n", | |
| ".xr-preview,\n", | |
| ".xr-attrs dt {\n", | |
| " white-space: nowrap;\n", | |
| " overflow: hidden;\n", | |
| " text-overflow: ellipsis;\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name:hover,\n", | |
| ".xr-var-dims:hover,\n", | |
| ".xr-var-dtype:hover,\n", | |
| ".xr-attrs dt:hover {\n", | |
| " overflow: visible;\n", | |
| " width: auto;\n", | |
| " z-index: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " display: none;\n", | |
| " background-color: var(--xr-background-color) !important;\n", | |
| " padding-bottom: 5px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", | |
| ".xr-var-data-in:checked ~ .xr-var-data {\n", | |
| " display: block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-data > table {\n", | |
| " float: right;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name span,\n", | |
| ".xr-var-data,\n", | |
| ".xr-attrs {\n", | |
| " padding-left: 25px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs,\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " grid-column: 1 / -1;\n", | |
| "}\n", | |
| "\n", | |
| "dl.xr-attrs {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 125px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt,\n", | |
| ".xr-attrs dd {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838, PCs_1: 50,\n", | |
| " X_pca_0: 2638, X_pca_1: 50, X_umap_0: 2638,\n", | |
| " X_umap_1: 2)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTTGCATGCCTCA...\n", | |
| " * vars (vars) object 'TNFRSF4' 'CPSF3L' ... 'S100B' 'PRMT2'\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 4 ... 1833 1834 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 5 6 ... 43 44 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 4 ... 2634 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 5 6 ... 44 45 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 4 ... 2634 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| "Data variables: (12/21)\n", | |
| " n_genes (obs) int64 781 1352 1131 960 ... 1227 622 454 724\n", | |
| " n_genes_by_counts (obs) int32 779 1352 1129 960 ... 1224 622 452 723\n", | |
| " total_counts (vars) float32 209.0 256.0 25.0 ... 50.0 207.0 745.0\n", | |
| " total_counts_mt (obs) float32 73.0 186.0 28.0 46.0 ... 37.0 21.0 16.0\n", | |
| " pct_counts_mt (obs) float32 3.018 3.794 0.8897 ... 2.055 0.8065\n", | |
| " leiden (obs) object 'CD8 T' 'B' 'CD4 T' ... 'B' 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " dispersions_norm (vars) float32 0.6654 2.955 4.353 ... 1.079 0.6291\n", | |
| " mean (vars) float64 -3.672e-10 -2.372e-10 ... -6.101e-10\n", | |
| " std (vars) float64 0.4245 0.4604 0.1195 ... 0.3999 0.7628\n", | |
| " PCs (PCs_0, PCs_1) float64 dask.array<chunksize=(1838, 50), meta=np.ndarray>\n", | |
| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray>\n", | |
| " X_umap (X_umap_0, X_umap_1) float32 dask.array<chunksize=(2638, 2), meta=np.ndarray></pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-40f204bb-9d12-4953-a501-7cef2ff63e6f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-40f204bb-9d12-4953-a501-7cef2ff63e6f' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>obs</span>: 2638</li><li><span class='xr-has-index'>vars</span>: 1838</li><li><span class='xr-has-index'>PCs_0</span>: 1838</li><li><span class='xr-has-index'>PCs_1</span>: 50</li><li><span class='xr-has-index'>X_pca_0</span>: 2638</li><li><span class='xr-has-index'>X_pca_1</span>: 50</li><li><span class='xr-has-index'>X_umap_0</span>: 2638</li><li><span class='xr-has-index'>X_umap_1</span>: 2</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-35d5ead3-1968-44da-b0f6-fe33bd3f30bd' class='xr-section-summary-in' type='checkbox' checked><label for='section-35d5ead3-1968-44da-b0f6-fe33bd3f30bd' class='xr-section-summary' >Coordinates: <span>(8)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>obs</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'AAACATACAACCAC-1' ... 'TTTGCATG...</div><input id='attrs-0754eb8e-898f-48a0-80e7-1948983b95b0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0754eb8e-898f-48a0-80e7-1948983b95b0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ceb3f4d3-0a17-4567-977e-34d5ad328e6a' class='xr-var-data-in' type='checkbox'><label for='data-ceb3f4d3-0a17-4567-977e-34d5ad328e6a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1', ...,\n", | |
| " 'TTTCTACTTCCTCG-1', 'TTTGCATGAGAGGC-1', 'TTTGCATGCCTCAC-1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>vars</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'TNFRSF4' 'CPSF3L' ... 'PRMT2'</div><input id='attrs-400f474f-1a46-49c0-89f2-88502da09e74' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-400f474f-1a46-49c0-89f2-88502da09e74' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4260ae46-a4cb-407b-a0eb-1a0fbb1b3620' class='xr-var-data-in' type='checkbox'><label for='data-4260ae46-a4cb-407b-a0eb-1a0fbb1b3620' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['TNFRSF4', 'CPSF3L', 'ATAD3C', ..., 'SLC19A1', 'S100B', 'PRMT2'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_0</span></div><div class='xr-var-dims'>(PCs_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 1834 1835 1836 1837</div><input id='attrs-6dd14986-4083-423c-a0d0-afbf1aea1ab2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6dd14986-4083-423c-a0d0-afbf1aea1ab2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-df364829-17f1-420c-92de-e436fd3eed13' class='xr-var-data-in' type='checkbox'><label for='data-df364829-17f1-420c-92de-e436fd3eed13' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 1835, 1836, 1837])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_1</span></div><div class='xr-var-dims'>(PCs_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-654e744a-2b10-42bf-afd5-aec7b5009287' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-654e744a-2b10-42bf-afd5-aec7b5009287' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1df61ecf-381d-4b89-a846-7e918782db3c' class='xr-var-data-in' type='checkbox'><label for='data-1df61ecf-381d-4b89-a846-7e918782db3c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_0</span></div><div class='xr-var-dims'>(X_pca_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-9daf5443-f8e8-4c0f-b6f7-a762e8d8e83d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9daf5443-f8e8-4c0f-b6f7-a762e8d8e83d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-79164950-9e33-4cc3-86ad-a9192d397d05' class='xr-var-data-in' type='checkbox'><label for='data-79164950-9e33-4cc3-86ad-a9192d397d05' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_1</span></div><div class='xr-var-dims'>(X_pca_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-34c3469b-0f6b-46ab-97dd-20272d82e91d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34c3469b-0f6b-46ab-97dd-20272d82e91d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ddc44805-2f14-4999-a715-414abc964e4f' class='xr-var-data-in' type='checkbox'><label for='data-ddc44805-2f14-4999-a715-414abc964e4f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_0</span></div><div class='xr-var-dims'>(X_umap_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-3531cd37-fcdf-490a-b3a8-eaf7fafd77aa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3531cd37-fcdf-490a-b3a8-eaf7fafd77aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1ace52ee-616b-434d-87d0-3ffdc008c8fa' class='xr-var-data-in' type='checkbox'><label for='data-1ace52ee-616b-434d-87d0-3ffdc008c8fa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_1</span></div><div class='xr-var-dims'>(X_umap_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1</div><input id='attrs-a43793e4-df2e-4578-a223-04cd257480b1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a43793e4-df2e-4578-a223-04cd257480b1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-82e13b21-430f-4ac5-909c-a80f5edc53d9' class='xr-var-data-in' type='checkbox'><label for='data-82e13b21-430f-4ac5-909c-a80f5edc53d9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0, 1])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-3be0ed0b-06ee-4484-8188-af3fbeda66b6' class='xr-section-summary-in' type='checkbox' ><label for='section-3be0ed0b-06ee-4484-8188-af3fbeda66b6' class='xr-section-summary' >Data variables: <span>(21)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>n_genes</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>781 1352 1131 960 ... 622 454 724</div><input id='attrs-91b3f789-a0a0-4c07-afc1-2c459dbf852e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-91b3f789-a0a0-4c07-afc1-2c459dbf852e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2cf051ca-621b-480a-8af0-ce585ebe6cf6' class='xr-var-data-in' type='checkbox'><label for='data-2cf051ca-621b-480a-8af0-ce585ebe6cf6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 781, 1352, 1131, ..., 622, 454, 724])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_genes_by_counts</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>779 1352 1129 960 ... 622 452 723</div><input id='attrs-63abd753-d977-4327-a84d-ec7df7c8f8a2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-63abd753-d977-4327-a84d-ec7df7c8f8a2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e621929f-0333-42c7-87ac-2f50a1393a71' class='xr-var-data-in' type='checkbox'><label for='data-e621929f-0333-42c7-87ac-2f50a1393a71' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 779, 1352, 1129, ..., 622, 452, 723], dtype=int32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>209.0 256.0 25.0 ... 207.0 745.0</div><input id='attrs-03ccda23-3734-4b1a-a561-54700c616b11' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-03ccda23-3734-4b1a-a561-54700c616b11' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7f2ef120-0d48-4e09-8f67-c5efa1c8f575' class='xr-var-data-in' type='checkbox'><label for='data-7f2ef120-0d48-4e09-8f67-c5efa1c8f575' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([209., 256., 25., ..., 50., 207., 745.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>73.0 186.0 28.0 ... 37.0 21.0 16.0</div><input id='attrs-ae4dc140-9ba1-4129-b378-9c2b66cd4416' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ae4dc140-9ba1-4129-b378-9c2b66cd4416' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e1dcd372-ff56-4f48-a1e4-528eb99534a8' class='xr-var-data-in' type='checkbox'><label for='data-e1dcd372-ff56-4f48-a1e4-528eb99534a8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 73., 186., 28., ..., 37., 21., 16.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>3.018 3.794 0.8897 ... 2.055 0.8065</div><input id='attrs-95e56f3f-f07f-448f-bfc0-790ac8482b2f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-95e56f3f-f07f-448f-bfc0-790ac8482b2f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ec7baaac-69aa-46da-8af9-07739d0ac435' class='xr-var-data-in' type='checkbox'><label for='data-ec7baaac-69aa-46da-8af9-07739d0ac435' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([3.017776 , 3.7935958 , 0.88973624, ..., 2.1971495 , 2.0547945 ,\n", | |
| " 0.80645156], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>leiden</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD8 T' 'B' 'CD4 T' ... 'B' 'CD4 T'</div><input id='attrs-9707d21c-fa17-40f8-8e68-766b43224527' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9707d21c-fa17-40f8-8e68-766b43224527' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2914e6c9-92b5-4537-9fe9-cfed3fc5dff7' class='xr-var-data-in' type='checkbox'><label for='data-2914e6c9-92b5-4537-9fe9-cfed3fc5dff7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD8 T', 'B', 'CD4 T', ..., 'B', 'B', 'CD4 T'], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>gene_ids</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'ENSG00000186827' ... 'ENSG00000...</div><input id='attrs-2e3050a1-83f3-4da9-8614-5dc44b2928c5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2e3050a1-83f3-4da9-8614-5dc44b2928c5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a364c76f-a4f3-497e-b192-aadd49b102c9' class='xr-var-data-in' type='checkbox'><label for='data-a364c76f-a4f3-497e-b192-aadd49b102c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['ENSG00000186827', 'ENSG00000127054', 'ENSG00000215915', ...,\n", | |
| " 'ENSG00000173638', 'ENSG00000160307', 'ENSG00000160310'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-9f141baf-69ff-4b31-9ada-f46816479c36' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9f141baf-69ff-4b31-9ada-f46816479c36' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2fdef647-f5c9-414e-a4af-d0420820ff6b' class='xr-var-data-in' type='checkbox'><label for='data-2fdef647-f5c9-414e-a4af-d0420820ff6b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mt</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... False False</div><input id='attrs-82d76200-4dc7-4258-9cc3-cee010c57f9d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-82d76200-4dc7-4258-9cc3-cee010c57f9d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8513ad56-aff6-4da2-b070-acb4ab4d6f48' class='xr-var-data-in' type='checkbox'><label for='data-8513ad56-aff6-4da2-b070-acb4ab4d6f48' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, ..., False, False, False])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-9b3690b7-d8dc-4539-b632-5436459ea9ca' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9b3690b7-d8dc-4539-b632-5436459ea9ca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-91ec8478-356a-42a9-b42b-3ada501273eb' class='xr-var-data-in' type='checkbox'><label for='data-91ec8478-356a-42a9-b42b-3ada501273eb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.07741 0.09481 ... 0.07667 0.2759</div><input id='attrs-4d3af8c3-b8de-48f1-a4d8-c43bd1c9eca1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4d3af8c3-b8de-48f1-a4d8-c43bd1c9eca1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cc4cae51-90d9-4034-b0ff-0d6283d241ad' class='xr-var-data-in' type='checkbox'><label for='data-cc4cae51-90d9-4034-b0ff-0d6283d241ad' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.0774074 , 0.09481481, 0.00925926, ..., 0.01851852, 0.07666667,\n", | |
| " 0.27592593], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_dropout_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>94.26 92.52 99.67 ... 96.52 78.22</div><input id='attrs-0a14711c-e1e3-411d-8457-546e4b294184' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0a14711c-e1e3-411d-8457-546e4b294184' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-78196f68-e929-4f65-848d-e673fe9c2ba9' class='xr-var-data-in' type='checkbox'><label for='data-78196f68-e929-4f65-848d-e673fe9c2ba9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([94.25925926, 92.51851852, 99.66666667, ..., 98.85185185,\n", | |
| " 96.51851852, 78.22222222])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>highly_variable</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>True True True ... True True True</div><input id='attrs-92015ec1-01df-4c53-9af8-1f59453c2283' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-92015ec1-01df-4c53-9af8-1f59453c2283' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aaffe647-87a3-4a58-849f-ad31fcbe52b6' class='xr-var-data-in' type='checkbox'><label for='data-aaffe647-87a3-4a58-849f-ad31fcbe52b6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ True, True, True, ..., True, True, True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>means</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.2774 0.3852 ... 0.2863 0.8166</div><input id='attrs-b6640632-43c2-44f7-ac85-cf8dc05d3305' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b6640632-43c2-44f7-ac85-cf8dc05d3305' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-10fe8820-09e0-4e28-85dc-e98050422c9b' class='xr-var-data-in' type='checkbox'><label for='data-10fe8820-09e0-4e28-85dc-e98050422c9b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.27741027, 0.38519408, 0.03825194, ..., 0.05895963, 0.28628215,\n", | |
| " 0.81664652])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>2.086 4.507 3.953 ... 3.043 2.774</div><input id='attrs-e396f600-a252-410e-a580-90e262ac7e7a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e396f600-a252-410e-a580-90e262ac7e7a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3cac6981-ab45-4e2f-b450-8775795a2773' class='xr-var-data-in' type='checkbox'><label for='data-3cac6981-ab45-4e2f-b450-8775795a2773' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([2.08604962, 4.5069874 , 3.95348633, ..., 3.23423114, 3.04299217,\n", | |
| " 2.77416884])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions_norm</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.6654 2.955 4.353 ... 1.079 0.6291</div><input id='attrs-4ecacd98-c451-45f1-aac4-df2d0534e99e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4ecacd98-c451-45f1-aac4-df2d0534e99e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8f0fb634-efb2-42f0-b8b7-1960b91a7c89' class='xr-var-data-in' type='checkbox'><label for='data-8f0fb634-efb2-42f0-b8b7-1960b91a7c89' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.66540575, 2.955005 , 4.3526073 , ..., 2.9324582 , 1.0787829 ,\n", | |
| " 0.62905824], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>-3.672e-10 ... -6.101e-10</div><input id='attrs-8b3397bb-3d3e-4714-8b47-3f5db290db06' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8b3397bb-3d3e-4714-8b47-3f5db290db06' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3356613b-6ffd-42b4-9558-4a520d0d273c' class='xr-var-data-in' type='checkbox'><label for='data-3356613b-6ffd-42b4-9558-4a520d0d273c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([-3.67206934e-10, -2.37243658e-10, 8.47298779e-12, ...,\n", | |
| " -2.02096928e-10, 5.99463886e-10, -6.10055121e-10])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>std</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.4245 0.4604 ... 0.3999 0.7628</div><input id='attrs-77a9a158-5435-4165-a33a-73e7844866ce' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-77a9a158-5435-4165-a33a-73e7844866ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eaaf1b29-4bf1-4b2b-ab50-6b277ca3c983' class='xr-var-data-in' type='checkbox'><label for='data-eaaf1b29-4bf1-4b2b-ab50-6b277ca3c983' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.42448087, 0.46041616, 0.11946545, ..., 0.17301715, 0.39994584,\n", | |
| " 0.7627529 ])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PCs</span></div><div class='xr-var-dims'>(PCs_0, PCs_1)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838, 50), meta=np.ndarray></div><input id='attrs-c5481f61-bb5b-47dd-a9b2-2506e05248be' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c5481f61-bb5b-47dd-a9b2-2506e05248be' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-64a0ef52-9add-4af2-8ed9-cb9dbed8698c' class='xr-var-data-in' type='checkbox'><label for='data-64a0ef52-9add-4af2-8ed9-cb9dbed8698c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"80\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"30\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"30\" y1=\"0\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 30.80809411591093,0.0 30.80809411591093,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"15.404047\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"50.808094\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,50.808094,60.000000)\">1838</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
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| " <th> Bytes </th>\n", | |
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| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838, PCs_1: 50,\n", | |
| " X_pca_0: 2638, X_pca_1: 50, X_umap_0: 2638,\n", | |
| " X_umap_1: 2)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTTGCATGCCTCA...\n", | |
| " * vars (vars) object 'TNFRSF4' 'CPSF3L' ... 'S100B' 'PRMT2'\n", | |
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| " * X_umap_0 (X_umap_0) int64 0 1 2 3 4 ... 2634 2635 2636 2637\n", | |
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| "Data variables: (12/21)\n", | |
| " n_genes (obs) int64 781 1352 1131 960 ... 1227 622 454 724\n", | |
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| " total_counts (vars) float32 209.0 256.0 25.0 ... 50.0 207.0 745.0\n", | |
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| " leiden (obs) object 'CD8 T' 'B' 'CD4 T' ... 'B' 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " dispersions_norm (vars) float32 0.6654 2.955 4.353 ... 1.079 0.6291\n", | |
| " mean (vars) float64 -3.672e-10 -2.372e-10 ... -6.101e-10\n", | |
| " std (vars) float64 0.4245 0.4604 0.1195 ... 0.3999 0.7628\n", | |
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| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray>\n", | |
| " X_umap (X_umap_0, X_umap_1) float32 dask.array<chunksize=(2638, 2), meta=np.ndarray>" | |
| ] | |
| }, | |
| "execution_count": 10, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata_ds = convert_anndata_to_xarray(results_file)\n", | |
| "adata_ds" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 11, | |
| "metadata": { | |
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| "name": "#%%\n" | |
| } | |
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| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
| " padding-right: 5px;\n", | |
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| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
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| " grid-column: 3;\n", | |
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| " padding-right: 10px;\n", | |
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| " font-weight: normal;\n", | |
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| "}\n", | |
| "\n", | |
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| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
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| " grid-column: 2;\n", | |
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| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
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| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.DataArray 'PCs' (PCs_0: 1838, PCs_1: 50)>\n", | |
| "dask.array<array, shape=(1838, 50), dtype=float64, chunksize=(1838, 50), chunktype=numpy.ndarray>\n", | |
| "Coordinates:\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 4 5 6 ... 1831 1832 1833 1834 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 5 6 7 8 9 ... 40 41 42 43 44 45 46 47 48 49</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'PCs'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>PCs_0</span>: 1838</li><li><span class='xr-has-index'>PCs_1</span>: 50</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-2e4f0056-fc69-4ac2-a438-210fbe53ef60' class='xr-array-in' type='checkbox' checked><label for='section-2e4f0056-fc69-4ac2-a438-210fbe53ef60' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array<chunksize=(1838, 50), meta=np.ndarray></span></div><div class='xr-array-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"80\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"30\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"30\" y1=\"0\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 30.80809411591093,0.0 30.80809411591093,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"15.404047\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"50.808094\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,50.808094,60.000000)\">1838</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></div></li><li class='xr-section-item'><input id='section-4528ddce-dab4-48ee-8def-29bfb22233e3' class='xr-section-summary-in' type='checkbox' checked><label for='section-4528ddce-dab4-48ee-8def-29bfb22233e3' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_0</span></div><div class='xr-var-dims'>(PCs_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 1834 1835 1836 1837</div><input id='attrs-9b768200-785f-4b47-a4d7-682397248abe' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9b768200-785f-4b47-a4d7-682397248abe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8fc95730-9524-448d-8c3d-70bb7326e3d1' class='xr-var-data-in' type='checkbox'><label for='data-8fc95730-9524-448d-8c3d-70bb7326e3d1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 1835, 1836, 1837])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_1</span></div><div class='xr-var-dims'>(PCs_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-428e7769-756b-4ad8-a6b6-ab27dc4ec322' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-428e7769-756b-4ad8-a6b6-ab27dc4ec322' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08840921-02c3-4597-a18e-1369a6b1f144' class='xr-var-data-in' type='checkbox'><label for='data-08840921-02c3-4597-a18e-1369a6b1f144' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-cb9179be-4974-4a84-9e0c-fc489b91eb36' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-cb9179be-4974-4a84-9e0c-fc489b91eb36' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.DataArray 'PCs' (PCs_0: 1838, PCs_1: 50)>\n", | |
| "dask.array<array, shape=(1838, 50), dtype=float64, chunksize=(1838, 50), chunktype=numpy.ndarray>\n", | |
| "Coordinates:\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 4 5 6 ... 1831 1832 1833 1834 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 5 6 7 8 9 ... 40 41 42 43 44 45 46 47 48 49" | |
| ] | |
| }, | |
| "execution_count": 11, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata_ds['PCs']" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Add Other Elements to the AnnData XArray DataSet\n", | |
| "\n", | |
| "AnnData is quite flexible and there are usually more records." | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "### Add rank_genes_groups\n", | |
| "\n", | |
| "In `adata.uns` there is a a `rank_genes_groups` key" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 12, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>CD4 T</th>\n", | |
| " <th>CD14 Monocytes</th>\n", | |
| " <th>B</th>\n", | |
| " <th>CD8 T</th>\n", | |
| " <th>NK</th>\n", | |
| " <th>FCGR3A Monocytes</th>\n", | |
| " <th>Dendritic</th>\n", | |
| " <th>Megakaryocytes</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>1.041539</td>\n", | |
| " <td>7.359957</td>\n", | |
| " <td>4.079535</td>\n", | |
| " <td>5.321771</td>\n", | |
| " <td>5.141453</td>\n", | |
| " <td>6.868872</td>\n", | |
| " <td>4.278315</td>\n", | |
| " <td>12.905741</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>2.668251</td>\n", | |
| " <td>6.166798</td>\n", | |
| " <td>7.749746</td>\n", | |
| " <td>4.925867</td>\n", | |
| " <td>4.886553</td>\n", | |
| " <td>7.695069</td>\n", | |
| " <td>4.434846</td>\n", | |
| " <td>11.863666</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>1.164884</td>\n", | |
| " <td>7.482893</td>\n", | |
| " <td>4.887034</td>\n", | |
| " <td>0.765132</td>\n", | |
| " <td>4.791256</td>\n", | |
| " <td>7.759242</td>\n", | |
| " <td>4.608550</td>\n", | |
| " <td>12.428451</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>1.017071</td>\n", | |
| " <td>5.334051</td>\n", | |
| " <td>5.518004</td>\n", | |
| " <td>4.195086</td>\n", | |
| " <td>3.645046</td>\n", | |
| " <td>4.807891</td>\n", | |
| " <td>4.237393</td>\n", | |
| " <td>13.035219</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>0.868595</td>\n", | |
| " <td>5.443555</td>\n", | |
| " <td>4.065814</td>\n", | |
| " <td>4.111341</td>\n", | |
| " <td>2.986083</td>\n", | |
| " <td>6.341140</td>\n", | |
| " <td>3.639149</td>\n", | |
| " <td>9.092909</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " CD4 T CD14 Monocytes B CD8 T NK FCGR3A Monocytes \\\n", | |
| "0 1.041539 7.359957 4.079535 5.321771 5.141453 6.868872 \n", | |
| "1 2.668251 6.166798 7.749746 4.925867 4.886553 7.695069 \n", | |
| "2 1.164884 7.482893 4.887034 0.765132 4.791256 7.759242 \n", | |
| "3 1.017071 5.334051 5.518004 4.195086 3.645046 4.807891 \n", | |
| "4 0.868595 5.443555 4.065814 4.111341 2.986083 6.341140 \n", | |
| "\n", | |
| " Dendritic Megakaryocytes \n", | |
| "0 4.278315 12.905741 \n", | |
| "1 4.434846 11.863666 \n", | |
| "2 4.608550 12.428451 \n", | |
| "3 4.237393 13.035219 \n", | |
| "4 3.639149 9.092909 " | |
| ] | |
| }, | |
| "execution_count": 12, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "pd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges']).head()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 13, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
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| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>CD4 T</th>\n", | |
| " <th>CD14 Monocytes</th>\n", | |
| " <th>B</th>\n", | |
| " <th>CD8 T</th>\n", | |
| " <th>NK</th>\n", | |
| " <th>FCGR3A Monocytes</th>\n", | |
| " <th>Dendritic</th>\n", | |
| " <th>Megakaryocytes</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>RPS12</td>\n", | |
| " <td>S100A9</td>\n", | |
| " <td>CD74</td>\n", | |
| " <td>CCL5</td>\n", | |
| " <td>LST1</td>\n", | |
| " <td>NKG7</td>\n", | |
| " <td>HLA-DPA1</td>\n", | |
| " <td>PF4</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>LDHB</td>\n", | |
| " <td>LYZ</td>\n", | |
| " <td>CD79A</td>\n", | |
| " <td>NKG7</td>\n", | |
| " <td>AIF1</td>\n", | |
| " <td>GZMB</td>\n", | |
| " <td>HLA-DPB1</td>\n", | |
| " <td>SDPR</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>RPS25</td>\n", | |
| " <td>S100A8</td>\n", | |
| " <td>HLA-DRA</td>\n", | |
| " <td>B2M</td>\n", | |
| " <td>FCER1G</td>\n", | |
| " <td>GNLY</td>\n", | |
| " <td>HLA-DRA</td>\n", | |
| " <td>GNG11</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>RPS27</td>\n", | |
| " <td>TYROBP</td>\n", | |
| " <td>CD79B</td>\n", | |
| " <td>CST7</td>\n", | |
| " <td>COTL1</td>\n", | |
| " <td>CTSW</td>\n", | |
| " <td>HLA-DRB1</td>\n", | |
| " <td>PPBP</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>RPS6</td>\n", | |
| " <td>FCN1</td>\n", | |
| " <td>HLA-DPB1</td>\n", | |
| " <td>GZMA</td>\n", | |
| " <td>FTH1</td>\n", | |
| " <td>PRF1</td>\n", | |
| " <td>CD74</td>\n", | |
| " <td>NRGN</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " CD4 T CD14 Monocytes B CD8 T NK FCGR3A Monocytes Dendritic \\\n", | |
| "0 RPS12 S100A9 CD74 CCL5 LST1 NKG7 HLA-DPA1 \n", | |
| "1 LDHB LYZ CD79A NKG7 AIF1 GZMB HLA-DPB1 \n", | |
| "2 RPS25 S100A8 HLA-DRA B2M FCER1G GNLY HLA-DRA \n", | |
| "3 RPS27 TYROBP CD79B CST7 COTL1 CTSW HLA-DRB1 \n", | |
| "4 RPS6 FCN1 HLA-DPB1 GZMA FTH1 PRF1 CD74 \n", | |
| "\n", | |
| " Megakaryocytes \n", | |
| "0 PF4 \n", | |
| "1 SDPR \n", | |
| "2 GNG11 \n", | |
| "3 PPBP \n", | |
| "4 NRGN " | |
| ] | |
| }, | |
| "execution_count": 13, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "pd.DataFrame(adata.uns['rank_genes_groups']['names']).head()" | |
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| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 2 3 ... 13711 13712 13713\n", | |
| "Data variables:\n", | |
| " CD4 T (rank_genes_groups) float32 1.042 2.668 ... -2.076 -2.819\n", | |
| " CD14 Monocytes (rank_genes_groups) float32 7.36 6.167 ... -2.032 -1.598\n", | |
| " B (rank_genes_groups) float32 4.08 7.75 ... -0.8629 -3.911\n", | |
| " CD8 T (rank_genes_groups) float32 5.322 4.926 ... -0.6679\n", | |
| " NK (rank_genes_groups) float32 5.141 4.887 ... -1.013 -1.202\n", | |
| " FCGR3A Monocytes (rank_genes_groups) float32 6.869 7.695 ... -1.337 -1.286\n", | |
| " Dendritic (rank_genes_groups) float32 4.278 4.435 ... -1.179\n", | |
| " Megakaryocytes (rank_genes_groups) float32 12.91 11.86 ... -3.965 -4.84</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-a1f1606f-c972-46a2-bab5-c19b84edb638' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a1f1606f-c972-46a2-bab5-c19b84edb638' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>rank_genes_groups</span>: 13714</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-b32a9642-fae2-41aa-a1cc-55c5571f4816' class='xr-section-summary-in' type='checkbox' checked><label for='section-b32a9642-fae2-41aa-a1cc-55c5571f4816' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>rank_genes_groups</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 ... 13710 13711 13712 13713</div><input id='attrs-e446212d-1633-460e-a866-e712e14eea5a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e446212d-1633-460e-a866-e712e14eea5a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b52846fb-71bd-41d1-bbe9-43fdae74fd30' class='xr-var-data-in' type='checkbox'><label for='data-b52846fb-71bd-41d1-bbe9-43fdae74fd30' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 13711, 13712, 13713])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-36f0919d-f895-4cb2-aca4-3ede8ff874b4' class='xr-section-summary-in' type='checkbox' checked><label for='section-36f0919d-f895-4cb2-aca4-3ede8ff874b4' class='xr-section-summary' >Data variables: <span>(8)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>1.042 2.668 1.165 ... -2.076 -2.819</div><input id='attrs-8a6a7a2a-a846-4903-89f5-76b2790f75c3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8a6a7a2a-a846-4903-89f5-76b2790f75c3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4285507c-fb0a-4e80-89cd-60dfeb87cd0d' class='xr-var-data-in' type='checkbox'><label for='data-4285507c-fb0a-4e80-89cd-60dfeb87cd0d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 1.0415391, 2.6682508, 1.1648842, ..., -4.3634076, -2.075822 ,\n", | |
| " -2.818502 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>7.36 6.167 7.483 ... -2.032 -1.598</div><input id='attrs-e0a4d0e2-b2b6-4207-9878-6a33c8e7dab0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e0a4d0e2-b2b6-4207-9878-6a33c8e7dab0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-57fbfe9e-83e8-4e7e-9831-b14a5197cd9b' class='xr-var-data-in' type='checkbox'><label for='data-57fbfe9e-83e8-4e7e-9831-b14a5197cd9b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 7.3599567, 6.1667976, 7.4828935, ..., -1.2195065, -2.0324383,\n", | |
| " -1.5976202], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.08 7.75 4.887 ... -0.8629 -3.911</div><input id='attrs-859e79c7-f77b-4305-bdba-0aa77b61136b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-859e79c7-f77b-4305-bdba-0aa77b61136b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b450f4e5-6ac2-4c2d-961f-967b5472e0d8' class='xr-var-data-in' type='checkbox'><label for='data-b450f4e5-6ac2-4c2d-961f-967b5472e0d8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.0795345, 7.749746 , 4.8870344, ..., -3.1592414, -0.8628794,\n", | |
| " -3.9112678], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.322 4.926 ... -0.7609 -0.6679</div><input id='attrs-b6bce8bc-a064-4276-b493-3c97f5e67c0b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b6bce8bc-a064-4276-b493-3c97f5e67c0b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e6a8069a-6ba2-4dc0-aa47-56ec07d1603f' class='xr-var-data-in' type='checkbox'><label for='data-e6a8069a-6ba2-4dc0-aa47-56ec07d1603f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.3217707 , 4.9258666 , 0.76513237, ..., -1.080934 ,\n", | |
| " -0.7609468 , -0.6679198 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.141 4.887 4.791 ... -1.013 -1.202</div><input id='attrs-caf0f56b-8d9b-4068-80c3-7f084975edeb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-caf0f56b-8d9b-4068-80c3-7f084975edeb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8fe22274-4826-458f-a267-c99af0beb490' class='xr-var-data-in' type='checkbox'><label for='data-8fe22274-4826-458f-a267-c99af0beb490' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.141453 , 4.8865533 , 4.791256 , ..., -0.97208005,\n", | |
| " -1.0129575 , -1.2016066 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>6.869 7.695 7.759 ... -1.337 -1.286</div><input id='attrs-e00161b4-9967-4e03-a1df-1bab685a3f89' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e00161b4-9967-4e03-a1df-1bab685a3f89' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-712aaedb-5956-41ba-9fc0-8017a4cd0193' class='xr-var-data-in' type='checkbox'><label for='data-712aaedb-5956-41ba-9fc0-8017a4cd0193' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 6.8688717, 7.6950693, 7.759242 , ..., -1.0524981, -1.33682 ,\n", | |
| " -1.2857121], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.278 4.435 ... -0.7723 -1.179</div><input id='attrs-5bf8acdc-cbee-4e87-aa90-2c98c395e453' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5bf8acdc-cbee-4e87-aa90-2c98c395e453' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e6ff85fe-db66-4307-be8f-bf666083e22f' class='xr-var-data-in' type='checkbox'><label for='data-e6ff85fe-db66-4307-be8f-bf666083e22f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.2783146 , 4.4348464 , 4.6085496 , ..., -0.7930738 ,\n", | |
| " -0.77232665, -1.1790817 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>12.91 11.86 12.43 ... -3.965 -4.84</div><input id='attrs-e2f4efaa-1aa0-4e23-8d4a-12699d0a834f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e2f4efaa-1aa0-4e23-8d4a-12699d0a834f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f1fd7f66-c322-4aa2-8587-2dc2ef2dadc2' class='xr-var-data-in' type='checkbox'><label for='data-f1fd7f66-c322-4aa2-8587-2dc2ef2dadc2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([12.905741 , 11.863666 , 12.428451 , ..., -5.350221 , -3.9652784,\n", | |
| " -4.8402567], dtype=float32)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-63502ecc-4d11-4099-88c9-c436f43470fc' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-63502ecc-4d11-4099-88c9-c436f43470fc' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 2 3 ... 13711 13712 13713\n", | |
| "Data variables:\n", | |
| " CD4 T (rank_genes_groups) float32 1.042 2.668 ... -2.076 -2.819\n", | |
| " CD14 Monocytes (rank_genes_groups) float32 7.36 6.167 ... -2.032 -1.598\n", | |
| " B (rank_genes_groups) float32 4.08 7.75 ... -0.8629 -3.911\n", | |
| " CD8 T (rank_genes_groups) float32 5.322 4.926 ... -0.6679\n", | |
| " NK (rank_genes_groups) float32 5.141 4.887 ... -1.013 -1.202\n", | |
| " FCGR3A Monocytes (rank_genes_groups) float32 6.869 7.695 ... -1.337 -1.286\n", | |
| " Dendritic (rank_genes_groups) float32 4.278 4.435 ... -1.179\n", | |
| " Megakaryocytes (rank_genes_groups) float32 12.91 11.86 ... -3.965 -4.84" | |
| ] | |
| }, | |
| "execution_count": 14, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "rank_genes_groups_logfoldchanges_ds = xr.Dataset.from_dataframe(\n", | |
| " pd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges'])).rename({'index': 'rank_genes_groups'})\n", | |
| "rank_genes_groups_logfoldchanges_ds" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 15, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
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| ".xr-section-summary-in:checked + label > span {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary,\n", | |
| ".xr-section-inline-details {\n", | |
| " padding-top: 4px;\n", | |
| " padding-bottom: 4px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-inline-details {\n", | |
| " grid-column: 2 / -1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-details {\n", | |
| " display: none;\n", | |
| " grid-column: 1 / -1;\n", | |
| " margin-bottom: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:checked ~ .xr-section-details {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-wrap {\n", | |
| " grid-column: 1 / -1;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 20px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-wrap > label {\n", | |
| " grid-column: 1;\n", | |
| " vertical-align: top;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-preview {\n", | |
| " color: var(--xr-font-color3);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-preview,\n", | |
| ".xr-array-data {\n", | |
| " padding: 0 5px !important;\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-data,\n", | |
| ".xr-array-in:checked ~ .xr-array-preview {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-in:checked ~ .xr-array-data,\n", | |
| ".xr-array-preview {\n", | |
| " display: inline-block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list {\n", | |
| " display: inline-block !important;\n", | |
| " list-style: none;\n", | |
| " padding: 0 !important;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li {\n", | |
| " display: inline-block;\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:before {\n", | |
| " content: '(';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:after {\n", | |
| " content: ')';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li:not(:last-child):after {\n", | |
| " content: ',';\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-has-index {\n", | |
| " font-weight: bold;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list,\n", | |
| ".xr-var-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > div,\n", | |
| ".xr-var-item label,\n", | |
| ".xr-var-item > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-even);\n", | |
| " margin-bottom: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-odd);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name {\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dims {\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dtype {\n", | |
| " grid-column: 3;\n", | |
| " text-align: right;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-preview {\n", | |
| " grid-column: 4;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name,\n", | |
| ".xr-var-dims,\n", | |
| ".xr-var-dtype,\n", | |
| ".xr-preview,\n", | |
| ".xr-attrs dt {\n", | |
| " white-space: nowrap;\n", | |
| " overflow: hidden;\n", | |
| " text-overflow: ellipsis;\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name:hover,\n", | |
| ".xr-var-dims:hover,\n", | |
| ".xr-var-dtype:hover,\n", | |
| ".xr-attrs dt:hover {\n", | |
| " overflow: visible;\n", | |
| " width: auto;\n", | |
| " z-index: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " display: none;\n", | |
| " background-color: var(--xr-background-color) !important;\n", | |
| " padding-bottom: 5px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", | |
| ".xr-var-data-in:checked ~ .xr-var-data {\n", | |
| " display: block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-data > table {\n", | |
| " float: right;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name span,\n", | |
| ".xr-var-data,\n", | |
| ".xr-attrs {\n", | |
| " padding-left: 25px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs,\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " grid-column: 1 / -1;\n", | |
| "}\n", | |
| "\n", | |
| "dl.xr-attrs {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 125px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt,\n", | |
| ".xr-attrs dd {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 2 3 ... 13711 13712 13713\n", | |
| "Data variables:\n", | |
| " CD4 T (rank_genes_groups) object 'RPS12' 'LDHB' ... 'CD74'\n", | |
| " CD14 Monocytes (rank_genes_groups) object 'S100A9' 'LYZ' ... 'MALAT1'\n", | |
| " B (rank_genes_groups) object 'CD74' 'CD79A' ... 'S100A4'\n", | |
| " CD8 T (rank_genes_groups) object 'CCL5' 'NKG7' ... 'TMSB10'\n", | |
| " NK (rank_genes_groups) object 'LST1' 'AIF1' ... 'RPL3'\n", | |
| " FCGR3A Monocytes (rank_genes_groups) object 'NKG7' 'GZMB' ... 'RPL32'\n", | |
| " Dendritic (rank_genes_groups) object 'HLA-DPA1' ... 'MALAT1'\n", | |
| " Megakaryocytes (rank_genes_groups) object 'PF4' 'SDPR' ... 'RPL10'</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-34c5fa7c-bfd8-4de2-95d8-6515a1ba5016' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-34c5fa7c-bfd8-4de2-95d8-6515a1ba5016' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>rank_genes_groups</span>: 13714</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-e5f99cc6-94ca-448d-9208-69d7efd27bb5' class='xr-section-summary-in' type='checkbox' checked><label for='section-e5f99cc6-94ca-448d-9208-69d7efd27bb5' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>rank_genes_groups</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 ... 13710 13711 13712 13713</div><input id='attrs-ca4a4415-9f27-4c9d-97fa-41edad9d0aad' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ca4a4415-9f27-4c9d-97fa-41edad9d0aad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7544ed61-de41-4152-9b6c-fc460e17d9f2' class='xr-var-data-in' type='checkbox'><label for='data-7544ed61-de41-4152-9b6c-fc460e17d9f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 13711, 13712, 13713])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2477c148-c59d-43cc-b69a-a5f74b3a333a' class='xr-section-summary-in' type='checkbox' checked><label for='section-2477c148-c59d-43cc-b69a-a5f74b3a333a' class='xr-section-summary' >Data variables: <span>(8)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'RPS12' 'LDHB' ... 'CYBA' 'CD74'</div><input id='attrs-b046bcde-5ae3-413c-81e8-27c7aa9e2d19' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b046bcde-5ae3-413c-81e8-27c7aa9e2d19' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-75734bcd-82c3-41a9-a11f-768ef7a17a75' class='xr-var-data-in' type='checkbox'><label for='data-75734bcd-82c3-41a9-a11f-768ef7a17a75' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['RPS12', 'LDHB', 'RPS25', ..., 'HLA-DRA', 'CYBA', 'CD74'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'S100A9' 'LYZ' ... 'MALAT1'</div><input id='attrs-ca0ef55e-b2fa-4e64-b506-53361743b794' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ca0ef55e-b2fa-4e64-b506-53361743b794' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-21b59841-f4c5-4a33-8eca-b842139f078a' class='xr-var-data-in' type='checkbox'><label for='data-21b59841-f4c5-4a33-8eca-b842139f078a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['S100A9', 'LYZ', 'S100A8', ..., 'RPS27', 'RPS27A', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD74' 'CD79A' ... 'S100A4'</div><input id='attrs-86cdff5f-7d1c-4e60-9cdc-f5157bef621c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-86cdff5f-7d1c-4e60-9cdc-f5157bef621c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-33fde664-7bfe-4c8f-8bc0-c9d93fb49468' class='xr-var-data-in' type='checkbox'><label for='data-33fde664-7bfe-4c8f-8bc0-c9d93fb49468' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD74', 'CD79A', 'HLA-DRA', ..., 'S100A6', 'TMSB4X', 'S100A4'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CCL5' 'NKG7' ... 'RPS11' 'TMSB10'</div><input id='attrs-0bd964a6-2cff-47f9-bae9-b22c55d7aaea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0bd964a6-2cff-47f9-bae9-b22c55d7aaea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e48aefaf-ff49-40df-bf5c-29041ec17b3e' class='xr-var-data-in' type='checkbox'><label for='data-e48aefaf-ff49-40df-bf5c-29041ec17b3e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CCL5', 'NKG7', 'B2M', ..., 'FTH1', 'RPS11', 'TMSB10'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'LST1' 'AIF1' ... 'RPL13' 'RPL3'</div><input id='attrs-ab938dcc-98bd-4032-ab3d-edfd30a09012' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ab938dcc-98bd-4032-ab3d-edfd30a09012' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b1424a11-55a9-4788-bb40-765a92727303' class='xr-var-data-in' type='checkbox'><label for='data-b1424a11-55a9-4788-bb40-765a92727303' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['LST1', 'AIF1', 'FCER1G', ..., 'RPL13A', 'RPL13', 'RPL3'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'NKG7' 'GZMB' ... 'RPL18A' 'RPL32'</div><input id='attrs-91399d8f-b3fb-4f66-921f-aa553773c842' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-91399d8f-b3fb-4f66-921f-aa553773c842' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-867fd47f-1bfe-465f-a1b1-31a94dfcd144' class='xr-var-data-in' type='checkbox'><label for='data-867fd47f-1bfe-465f-a1b1-31a94dfcd144' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['NKG7', 'GZMB', 'GNLY', ..., 'RPL28', 'RPL18A', 'RPL32'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'HLA-DPA1' 'HLA-DPB1' ... 'MALAT1'</div><input id='attrs-b01e76a5-c85a-47d7-a930-0578c466287a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b01e76a5-c85a-47d7-a930-0578c466287a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-882ee0b3-3dd1-4ac4-b676-9ad7101a1532' class='xr-var-data-in' type='checkbox'><label for='data-882ee0b3-3dd1-4ac4-b676-9ad7101a1532' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['HLA-DPA1', 'HLA-DPB1', 'HLA-DRA', ..., 'RPL21', 'RPS27', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'PF4' 'SDPR' ... 'MALAT1' 'RPL10'</div><input id='attrs-97ece1da-3a28-4996-a81a-ca9934bc643f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-97ece1da-3a28-4996-a81a-ca9934bc643f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2ed4c215-4e71-4f69-8300-34d70f8e0370' class='xr-var-data-in' type='checkbox'><label for='data-2ed4c215-4e71-4f69-8300-34d70f8e0370' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['PF4', 'SDPR', 'GNG11', ..., 'RPL11', 'MALAT1', 'RPL10'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-fda14ac8-a895-492f-896f-d6301820957e' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-fda14ac8-a895-492f-896f-d6301820957e' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 2 3 ... 13711 13712 13713\n", | |
| "Data variables:\n", | |
| " CD4 T (rank_genes_groups) object 'RPS12' 'LDHB' ... 'CD74'\n", | |
| " CD14 Monocytes (rank_genes_groups) object 'S100A9' 'LYZ' ... 'MALAT1'\n", | |
| " B (rank_genes_groups) object 'CD74' 'CD79A' ... 'S100A4'\n", | |
| " CD8 T (rank_genes_groups) object 'CCL5' 'NKG7' ... 'TMSB10'\n", | |
| " NK (rank_genes_groups) object 'LST1' 'AIF1' ... 'RPL3'\n", | |
| " FCGR3A Monocytes (rank_genes_groups) object 'NKG7' 'GZMB' ... 'RPL32'\n", | |
| " Dendritic (rank_genes_groups) object 'HLA-DPA1' ... 'MALAT1'\n", | |
| " Megakaryocytes (rank_genes_groups) object 'PF4' 'SDPR' ... 'RPL10'" | |
| ] | |
| }, | |
| "execution_count": 15, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "rank_genes_groups_names_ds = xr.Dataset.from_dataframe(pd.DataFrame(adata.uns['rank_genes_groups']['names'])).rename(\n", | |
| " {'index': 'rank_genes_groups'})\n", | |
| "rank_genes_groups_names_ds" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "### Add genes back to the AnnData XR Dataset" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 16, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "adata_ds.coords['rank_genes_groups'] = rank_genes_groups_logfoldchanges_ds.coords['rank_genes_groups'].data" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 17, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "for k in list(rank_genes_groups_logfoldchanges_ds.data_vars.keys()):\n", | |
| " adata_ds[f'logfoldchanges_{k}'] = rank_genes_groups_logfoldchanges_ds[k]\n", | |
| "\n", | |
| "for k in list(rank_genes_groups_names_ds.data_vars.keys()):\n", | |
| " adata_ds[f'names_{k}'] = rank_genes_groups_names_ds[k]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 18, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "gene_groups = list(pd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges']).columns)\n", | |
| "coords = {}\n", | |
| "coords['genes_groups'] = np.arange(len(gene_groups))\n", | |
| "adata_ds.coords.update(coords)\n", | |
| "adata_ds['genes_groups'] = xr.DataArray(coords=coords, dims=list(coords.keys()), data=np.array(gene_groups))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 19, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
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| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838,\n", | |
| " PCs_1: 50, X_pca_0: 2638, X_pca_1: 50,\n", | |
| " X_umap_0: 2638, X_umap_1: 2,\n", | |
| " rank_genes_groups: 13714, genes_groups: 8)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTT...\n", | |
| " * vars (vars) object 'TNFRSF4' ... 'PRMT2'\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 ... 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 ... 13713\n", | |
| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
| "Data variables: (12/37)\n", | |
| " n_genes (obs) int64 781 1352 1131 ... 622 454 724\n", | |
| " n_genes_by_counts (obs) int32 779 1352 1129 ... 622 452 723\n", | |
| " total_counts (vars) float32 209.0 256.0 ... 207.0 745.0\n", | |
| " total_counts_mt (obs) float32 73.0 186.0 28.0 ... 21.0 16.0\n", | |
| " pct_counts_mt (obs) float32 3.018 3.794 ... 2.055 0.8065\n", | |
| " leiden (obs) object 'CD8 T' 'B' ... 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " names_B (rank_genes_groups) object 'CD74' ... 'S...\n", | |
| " names_CD8 T (rank_genes_groups) object 'CCL5' ... 'T...\n", | |
| " names_NK (rank_genes_groups) object 'LST1' ... 'R...\n", | |
| " names_FCGR3A Monocytes (rank_genes_groups) object 'NKG7' ... 'R...\n", | |
| " names_Dendritic (rank_genes_groups) object 'HLA-DPA1' .....\n", | |
| " names_Megakaryocytes (rank_genes_groups) object 'PF4' ... 'RP...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-6f45675b-448c-4d77-ad98-71c68746e544' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-6f45675b-448c-4d77-ad98-71c68746e544' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>obs</span>: 2638</li><li><span class='xr-has-index'>vars</span>: 1838</li><li><span class='xr-has-index'>PCs_0</span>: 1838</li><li><span class='xr-has-index'>PCs_1</span>: 50</li><li><span class='xr-has-index'>X_pca_0</span>: 2638</li><li><span class='xr-has-index'>X_pca_1</span>: 50</li><li><span class='xr-has-index'>X_umap_0</span>: 2638</li><li><span class='xr-has-index'>X_umap_1</span>: 2</li><li><span class='xr-has-index'>rank_genes_groups</span>: 13714</li><li><span class='xr-has-index'>genes_groups</span>: 8</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-12f1d86b-2e84-4a43-99aa-50687ed65a55' class='xr-section-summary-in' type='checkbox' checked><label for='section-12f1d86b-2e84-4a43-99aa-50687ed65a55' class='xr-section-summary' >Coordinates: <span>(10)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>obs</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'AAACATACAACCAC-1' ... 'TTTGCATG...</div><input id='attrs-8c5638ef-99d8-49a5-a02c-6c3d75bf1324' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8c5638ef-99d8-49a5-a02c-6c3d75bf1324' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-36e1c7b2-c121-4ad7-a049-66f5d7e9318c' class='xr-var-data-in' type='checkbox'><label for='data-36e1c7b2-c121-4ad7-a049-66f5d7e9318c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1', ...,\n", | |
| " 'TTTCTACTTCCTCG-1', 'TTTGCATGAGAGGC-1', 'TTTGCATGCCTCAC-1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>vars</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'TNFRSF4' 'CPSF3L' ... 'PRMT2'</div><input id='attrs-d1634498-cca8-4bb2-bb1c-d91385cde734' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d1634498-cca8-4bb2-bb1c-d91385cde734' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-53339235-2300-4826-bfb8-be73cbd36251' class='xr-var-data-in' type='checkbox'><label for='data-53339235-2300-4826-bfb8-be73cbd36251' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['TNFRSF4', 'CPSF3L', 'ATAD3C', ..., 'SLC19A1', 'S100B', 'PRMT2'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_0</span></div><div class='xr-var-dims'>(PCs_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 1834 1835 1836 1837</div><input id='attrs-a7de00b1-88df-4aa8-818c-2f617f9a188e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a7de00b1-88df-4aa8-818c-2f617f9a188e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b29f8dc7-da91-4e93-b4ab-2a05a3af4820' class='xr-var-data-in' type='checkbox'><label for='data-b29f8dc7-da91-4e93-b4ab-2a05a3af4820' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 1835, 1836, 1837])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_1</span></div><div class='xr-var-dims'>(PCs_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-0bb95810-a15b-4047-bc95-f9f95ed55114' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0bb95810-a15b-4047-bc95-f9f95ed55114' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1b3fb6ae-ac1d-46bc-a526-f67020dd9c7e' class='xr-var-data-in' type='checkbox'><label for='data-1b3fb6ae-ac1d-46bc-a526-f67020dd9c7e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_0</span></div><div class='xr-var-dims'>(X_pca_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-93ec7e0b-8469-4cd4-acd0-4375552c5a2c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-93ec7e0b-8469-4cd4-acd0-4375552c5a2c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf371d71-014a-4fe6-86eb-a9032f5b1af7' class='xr-var-data-in' type='checkbox'><label for='data-bf371d71-014a-4fe6-86eb-a9032f5b1af7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_1</span></div><div class='xr-var-dims'>(X_pca_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-2cf9e48c-8c39-45e0-be0e-8b1f51c2d41e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2cf9e48c-8c39-45e0-be0e-8b1f51c2d41e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7d541e85-e6f9-4b68-b5d2-6a66b2c84121' class='xr-var-data-in' type='checkbox'><label for='data-7d541e85-e6f9-4b68-b5d2-6a66b2c84121' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_0</span></div><div class='xr-var-dims'>(X_umap_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-5dc7f56b-88b7-4510-8f47-cd9d929d675a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5dc7f56b-88b7-4510-8f47-cd9d929d675a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cccac589-f9d7-4129-b821-73332422eccc' class='xr-var-data-in' type='checkbox'><label for='data-cccac589-f9d7-4129-b821-73332422eccc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_1</span></div><div class='xr-var-dims'>(X_umap_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1</div><input id='attrs-3bc1fb59-21d8-4b6e-b52a-a53385786e13' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3bc1fb59-21d8-4b6e-b52a-a53385786e13' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ed85e505-bf42-4110-beca-19365f72e31e' class='xr-var-data-in' type='checkbox'><label for='data-ed85e505-bf42-4110-beca-19365f72e31e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0, 1])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>rank_genes_groups</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 ... 13710 13711 13712 13713</div><input id='attrs-53c60bb4-bd1a-497a-9a9a-20d63d492912' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-53c60bb4-bd1a-497a-9a9a-20d63d492912' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f4fdb202-5ec0-4860-905a-5c0a6e1ad336' class='xr-var-data-in' type='checkbox'><label for='data-f4fdb202-5ec0-4860-905a-5c0a6e1ad336' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 13711, 13712, 13713])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genes_groups</span></div><div class='xr-var-dims'>(genes_groups)</div><div class='xr-var-dtype'><U16</div><div class='xr-var-preview xr-preview'>'CD4 T' ... 'Megakaryocytes'</div><input id='attrs-f941f0d4-b669-47ef-a98c-7895500584ba' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f941f0d4-b669-47ef-a98c-7895500584ba' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-28ac6955-b010-4b1b-b65f-d0536c5247d0' class='xr-var-data-in' type='checkbox'><label for='data-28ac6955-b010-4b1b-b65f-d0536c5247d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD4 T', 'CD14 Monocytes', 'B', 'CD8 T', 'NK', 'FCGR3A Monocytes',\n", | |
| " 'Dendritic', 'Megakaryocytes'], dtype='<U16')</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-0d96b2c3-307a-4e45-91b7-ba5ef6bbd499' class='xr-section-summary-in' type='checkbox' ><label for='section-0d96b2c3-307a-4e45-91b7-ba5ef6bbd499' class='xr-section-summary' >Data variables: <span>(37)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>n_genes</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>781 1352 1131 960 ... 622 454 724</div><input id='attrs-f1de4596-6e05-42fd-99d7-e9feb3b11fa7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f1de4596-6e05-42fd-99d7-e9feb3b11fa7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c22cab6f-7671-4864-ae75-cc26c314ae97' class='xr-var-data-in' type='checkbox'><label for='data-c22cab6f-7671-4864-ae75-cc26c314ae97' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 781, 1352, 1131, ..., 622, 454, 724])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_genes_by_counts</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>779 1352 1129 960 ... 622 452 723</div><input id='attrs-c74ae3b4-dc14-4555-a18b-2e2198ab6912' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c74ae3b4-dc14-4555-a18b-2e2198ab6912' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-43fbeab3-c9b8-4d8a-ba14-66043533626f' class='xr-var-data-in' type='checkbox'><label for='data-43fbeab3-c9b8-4d8a-ba14-66043533626f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 779, 1352, 1129, ..., 622, 452, 723], dtype=int32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>209.0 256.0 25.0 ... 207.0 745.0</div><input id='attrs-687a26b4-1e1d-414f-9d0f-fd47a65852a0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-687a26b4-1e1d-414f-9d0f-fd47a65852a0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0ebd90b1-7cb4-4d3d-8038-118727ab768d' class='xr-var-data-in' type='checkbox'><label for='data-0ebd90b1-7cb4-4d3d-8038-118727ab768d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([209., 256., 25., ..., 50., 207., 745.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>73.0 186.0 28.0 ... 37.0 21.0 16.0</div><input id='attrs-5f4163fa-7f73-4393-912e-27ae31006fec' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5f4163fa-7f73-4393-912e-27ae31006fec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-58fc3189-db03-457c-b6c1-78a6b60974e2' class='xr-var-data-in' type='checkbox'><label for='data-58fc3189-db03-457c-b6c1-78a6b60974e2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 73., 186., 28., ..., 37., 21., 16.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>3.018 3.794 0.8897 ... 2.055 0.8065</div><input id='attrs-d0f45a9a-0a7c-4c2c-806b-0f173dab9042' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d0f45a9a-0a7c-4c2c-806b-0f173dab9042' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0db2cebd-3ef0-43ea-9709-ba40a8a2c4f4' class='xr-var-data-in' type='checkbox'><label for='data-0db2cebd-3ef0-43ea-9709-ba40a8a2c4f4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([3.017776 , 3.7935958 , 0.88973624, ..., 2.1971495 , 2.0547945 ,\n", | |
| " 0.80645156], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>leiden</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD8 T' 'B' 'CD4 T' ... 'B' 'CD4 T'</div><input id='attrs-706581b8-db1a-4805-a701-2d608f3be912' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-706581b8-db1a-4805-a701-2d608f3be912' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2c8032bd-bbda-4c59-a2db-4c3309e4471d' class='xr-var-data-in' type='checkbox'><label for='data-2c8032bd-bbda-4c59-a2db-4c3309e4471d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD8 T', 'B', 'CD4 T', ..., 'B', 'B', 'CD4 T'], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>gene_ids</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'ENSG00000186827' ... 'ENSG00000...</div><input id='attrs-4a7ab54b-dcbe-4e1b-a1fb-2f911b0af14a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4a7ab54b-dcbe-4e1b-a1fb-2f911b0af14a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-159e99f2-8b5a-4cea-8cc8-ddf451f86de8' class='xr-var-data-in' type='checkbox'><label for='data-159e99f2-8b5a-4cea-8cc8-ddf451f86de8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['ENSG00000186827', 'ENSG00000127054', 'ENSG00000215915', ...,\n", | |
| " 'ENSG00000173638', 'ENSG00000160307', 'ENSG00000160310'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-4136cb7b-4d48-4440-b468-1bdcdee9c638' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4136cb7b-4d48-4440-b468-1bdcdee9c638' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-72ea3170-8c5f-4422-ad10-392e627eca52' class='xr-var-data-in' type='checkbox'><label for='data-72ea3170-8c5f-4422-ad10-392e627eca52' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mt</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... False False</div><input id='attrs-822646f5-25ea-40ee-9d2e-bac38526c32c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-822646f5-25ea-40ee-9d2e-bac38526c32c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ecc9b2d0-0635-4876-8730-1a41847815a8' class='xr-var-data-in' type='checkbox'><label for='data-ecc9b2d0-0635-4876-8730-1a41847815a8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, ..., False, False, False])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-f84e91f4-7e0d-4cbf-975d-9c198c4fdf79' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f84e91f4-7e0d-4cbf-975d-9c198c4fdf79' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eef94d8b-8654-4afd-b768-dfcdfd65b054' class='xr-var-data-in' type='checkbox'><label for='data-eef94d8b-8654-4afd-b768-dfcdfd65b054' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.07741 0.09481 ... 0.07667 0.2759</div><input id='attrs-c1816ebb-5ff6-429e-b9e9-140ee88ba4ab' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c1816ebb-5ff6-429e-b9e9-140ee88ba4ab' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fe3bd2fd-02fa-4877-a27c-dc21f6a0775d' class='xr-var-data-in' type='checkbox'><label for='data-fe3bd2fd-02fa-4877-a27c-dc21f6a0775d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.0774074 , 0.09481481, 0.00925926, ..., 0.01851852, 0.07666667,\n", | |
| " 0.27592593], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_dropout_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>94.26 92.52 99.67 ... 96.52 78.22</div><input id='attrs-3f084427-a352-4cea-96b5-624ae4231536' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3f084427-a352-4cea-96b5-624ae4231536' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee98e47b-7012-4d86-8a8b-a7d768faf400' class='xr-var-data-in' type='checkbox'><label for='data-ee98e47b-7012-4d86-8a8b-a7d768faf400' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([94.25925926, 92.51851852, 99.66666667, ..., 98.85185185,\n", | |
| " 96.51851852, 78.22222222])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>highly_variable</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>True True True ... True True True</div><input id='attrs-8acbba36-94ea-4a5e-86fa-f1916e9cedd7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8acbba36-94ea-4a5e-86fa-f1916e9cedd7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-06bfb50e-f99d-410e-af52-36224838e96a' class='xr-var-data-in' type='checkbox'><label for='data-06bfb50e-f99d-410e-af52-36224838e96a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ True, True, True, ..., True, True, True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>means</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.2774 0.3852 ... 0.2863 0.8166</div><input id='attrs-db334701-f813-40ac-9823-f9d1b6a6b322' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-db334701-f813-40ac-9823-f9d1b6a6b322' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08b01ac5-ff78-4c55-88ea-a7689e73aadf' class='xr-var-data-in' type='checkbox'><label for='data-08b01ac5-ff78-4c55-88ea-a7689e73aadf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.27741027, 0.38519408, 0.03825194, ..., 0.05895963, 0.28628215,\n", | |
| " 0.81664652])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>2.086 4.507 3.953 ... 3.043 2.774</div><input id='attrs-26f0493c-fafb-4787-95d8-98f91580526b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-26f0493c-fafb-4787-95d8-98f91580526b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8ede2cc-ce47-44b2-b00f-f9d064cd46a9' class='xr-var-data-in' type='checkbox'><label for='data-b8ede2cc-ce47-44b2-b00f-f9d064cd46a9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([2.08604962, 4.5069874 , 3.95348633, ..., 3.23423114, 3.04299217,\n", | |
| " 2.77416884])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions_norm</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.6654 2.955 4.353 ... 1.079 0.6291</div><input id='attrs-5fee528b-a5a5-4bd2-a2cc-cfc4c5c12348' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5fee528b-a5a5-4bd2-a2cc-cfc4c5c12348' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6666bf54-3e78-41ad-8e3d-035fe83043d0' class='xr-var-data-in' type='checkbox'><label for='data-6666bf54-3e78-41ad-8e3d-035fe83043d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.66540575, 2.955005 , 4.3526073 , ..., 2.9324582 , 1.0787829 ,\n", | |
| " 0.62905824], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>-3.672e-10 ... -6.101e-10</div><input id='attrs-61b635fc-f54d-4b7e-87ba-9c2ea777f3d4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-61b635fc-f54d-4b7e-87ba-9c2ea777f3d4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2a584eb2-dca0-43e9-b2d9-2cd95b146b85' class='xr-var-data-in' type='checkbox'><label for='data-2a584eb2-dca0-43e9-b2d9-2cd95b146b85' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([-3.67206934e-10, -2.37243658e-10, 8.47298779e-12, ...,\n", | |
| " -2.02096928e-10, 5.99463886e-10, -6.10055121e-10])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>std</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.4245 0.4604 ... 0.3999 0.7628</div><input id='attrs-532b055d-f9cb-47b9-aae4-f69e330c8884' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-532b055d-f9cb-47b9-aae4-f69e330c8884' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3660bb4-2cc5-447b-9719-e965b8319cd4' class='xr-var-data-in' type='checkbox'><label for='data-c3660bb4-2cc5-447b-9719-e965b8319cd4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.42448087, 0.46041616, 0.11946545, ..., 0.17301715, 0.39994584,\n", | |
| " 0.7627529 ])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PCs</span></div><div class='xr-var-dims'>(PCs_0, PCs_1)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838, 50), meta=np.ndarray></div><input id='attrs-bba42277-fae7-458d-aac9-7a1f19edb519' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bba42277-fae7-458d-aac9-7a1f19edb519' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dac4e3ff-a0b8-4ad5-b6bb-f7ca563d7efd' class='xr-var-data-in' type='checkbox'><label for='data-dac4e3ff-a0b8-4ad5-b6bb-f7ca563d7efd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"80\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"30\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"30\" y1=\"0\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 30.80809411591093,0.0 30.80809411591093,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"15.404047\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"50.808094\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,50.808094,60.000000)\">1838</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_pca</span></div><div class='xr-var-dims'>(X_pca_0, X_pca_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 50), meta=np.ndarray></div><input id='attrs-3be5c4d2-1fe4-4068-881a-f3c8b42de26a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3be5c4d2-1fe4-4068-881a-f3c8b42de26a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-99938b57-7ff8-441e-b6dd-a09dce75cf89' class='xr-var-data-in' type='checkbox'><label for='data-99938b57-7ff8-441e-b6dd-a09dce75cf89' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"78\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"28\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"28\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"28\" y1=\"0\" x2=\"28\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 28.72981340784082,0.0 28.72981340784082,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"14.364907\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"48.729813\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,48.729813,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_umap</span></div><div class='xr-var-dims'>(X_umap_0, X_umap_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 2), meta=np.ndarray></div><input id='attrs-3715124b-2317-4f19-9405-9e9785914b65' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3715124b-2317-4f19-9405-9e9785914b65' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86dd7146-aba6-4283-af67-03bfb752107e' class='xr-var-data-in' type='checkbox'><label for='data-86dd7146-aba6-4283-af67-03bfb752107e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"75\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"12.706308\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >2</text>\n", | |
| " <text x=\"45.412617\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,45.412617,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>1.042 2.668 1.165 ... -2.076 -2.819</div><input id='attrs-da4b6524-a6fd-42fb-be21-a57e5eb6aea2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da4b6524-a6fd-42fb-be21-a57e5eb6aea2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a471ff85-a14a-44bf-ba72-664b1fc50b24' class='xr-var-data-in' type='checkbox'><label for='data-a471ff85-a14a-44bf-ba72-664b1fc50b24' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 1.0415391, 2.6682508, 1.1648842, ..., -4.3634076, -2.075822 ,\n", | |
| " -2.818502 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>7.36 6.167 7.483 ... -2.032 -1.598</div><input id='attrs-573d9659-c5a4-43b0-9a5d-036ef449a686' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-573d9659-c5a4-43b0-9a5d-036ef449a686' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2ecbeb62-3b65-4cde-b3bf-4c326031fa49' class='xr-var-data-in' type='checkbox'><label for='data-2ecbeb62-3b65-4cde-b3bf-4c326031fa49' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 7.3599567, 6.1667976, 7.4828935, ..., -1.2195065, -2.0324383,\n", | |
| " -1.5976202], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.08 7.75 4.887 ... -0.8629 -3.911</div><input id='attrs-27f85f17-8d81-4047-a089-c4490029c01f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-27f85f17-8d81-4047-a089-c4490029c01f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5d50d1c4-c474-471c-9dd9-0320dd89c085' class='xr-var-data-in' type='checkbox'><label for='data-5d50d1c4-c474-471c-9dd9-0320dd89c085' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.0795345, 7.749746 , 4.8870344, ..., -3.1592414, -0.8628794,\n", | |
| " -3.9112678], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.322 4.926 ... -0.7609 -0.6679</div><input id='attrs-1a9a14a2-db0a-4497-bddc-7012fcfe4890' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1a9a14a2-db0a-4497-bddc-7012fcfe4890' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3bdb5003-b48e-4c6c-83c0-73c20821b73e' class='xr-var-data-in' type='checkbox'><label for='data-3bdb5003-b48e-4c6c-83c0-73c20821b73e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.3217707 , 4.9258666 , 0.76513237, ..., -1.080934 ,\n", | |
| " -0.7609468 , -0.6679198 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.141 4.887 4.791 ... -1.013 -1.202</div><input id='attrs-e0fad973-79d8-452b-b0d2-6666cec11d9a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e0fad973-79d8-452b-b0d2-6666cec11d9a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f712e395-f885-41fd-abe7-74105e21afce' class='xr-var-data-in' type='checkbox'><label for='data-f712e395-f885-41fd-abe7-74105e21afce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.141453 , 4.8865533 , 4.791256 , ..., -0.97208005,\n", | |
| " -1.0129575 , -1.2016066 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>6.869 7.695 7.759 ... -1.337 -1.286</div><input id='attrs-67ec6048-9bcd-4057-aa3c-e827191211ca' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-67ec6048-9bcd-4057-aa3c-e827191211ca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-466e4b35-942c-42a9-b490-e19751670a38' class='xr-var-data-in' type='checkbox'><label for='data-466e4b35-942c-42a9-b490-e19751670a38' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 6.8688717, 7.6950693, 7.759242 , ..., -1.0524981, -1.33682 ,\n", | |
| " -1.2857121], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.278 4.435 ... -0.7723 -1.179</div><input id='attrs-4b893248-3c4e-4763-861b-9e52b6a173aa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4b893248-3c4e-4763-861b-9e52b6a173aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8e52a2c-346a-4ba2-880d-3f361c7b7520' class='xr-var-data-in' type='checkbox'><label for='data-e8e52a2c-346a-4ba2-880d-3f361c7b7520' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.2783146 , 4.4348464 , 4.6085496 , ..., -0.7930738 ,\n", | |
| " -0.77232665, -1.1790817 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>12.91 11.86 12.43 ... -3.965 -4.84</div><input id='attrs-635819a8-b0f9-42a1-a36b-35685a17ec00' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-635819a8-b0f9-42a1-a36b-35685a17ec00' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b07e35e2-b577-400f-9f7b-00740bcf0a8c' class='xr-var-data-in' type='checkbox'><label for='data-b07e35e2-b577-400f-9f7b-00740bcf0a8c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([12.905741 , 11.863666 , 12.428451 , ..., -5.350221 , -3.9652784,\n", | |
| " -4.8402567], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'RPS12' 'LDHB' ... 'CYBA' 'CD74'</div><input id='attrs-dfafa678-56c5-41c1-bd73-31dfbf84c020' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dfafa678-56c5-41c1-bd73-31dfbf84c020' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-755db6d4-9422-4280-9592-3ee366f941f0' class='xr-var-data-in' type='checkbox'><label for='data-755db6d4-9422-4280-9592-3ee366f941f0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['RPS12', 'LDHB', 'RPS25', ..., 'HLA-DRA', 'CYBA', 'CD74'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'S100A9' 'LYZ' ... 'MALAT1'</div><input id='attrs-bbe9f7b6-f53a-4498-89dc-423f0d05f131' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bbe9f7b6-f53a-4498-89dc-423f0d05f131' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-231327f6-7377-44c8-bf10-2035154c362d' class='xr-var-data-in' type='checkbox'><label for='data-231327f6-7377-44c8-bf10-2035154c362d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['S100A9', 'LYZ', 'S100A8', ..., 'RPS27', 'RPS27A', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD74' 'CD79A' ... 'S100A4'</div><input id='attrs-14c1edd6-c4eb-4bbb-a212-79378007d8cb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-14c1edd6-c4eb-4bbb-a212-79378007d8cb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-37592dbe-00c7-46a9-897f-71b791d613d5' class='xr-var-data-in' type='checkbox'><label for='data-37592dbe-00c7-46a9-897f-71b791d613d5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD74', 'CD79A', 'HLA-DRA', ..., 'S100A6', 'TMSB4X', 'S100A4'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CCL5' 'NKG7' ... 'RPS11' 'TMSB10'</div><input id='attrs-7c09a013-5616-49ea-b0e5-a10ee8aa29ab' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7c09a013-5616-49ea-b0e5-a10ee8aa29ab' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a1ef5ff3-7fe4-4608-a630-de54d3151bef' class='xr-var-data-in' type='checkbox'><label for='data-a1ef5ff3-7fe4-4608-a630-de54d3151bef' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CCL5', 'NKG7', 'B2M', ..., 'FTH1', 'RPS11', 'TMSB10'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'LST1' 'AIF1' ... 'RPL13' 'RPL3'</div><input id='attrs-525d7d93-0c82-49ff-b7d7-e355d59b910b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-525d7d93-0c82-49ff-b7d7-e355d59b910b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8b7ca47a-3b64-43e6-973c-ffc7af79a3a1' class='xr-var-data-in' type='checkbox'><label for='data-8b7ca47a-3b64-43e6-973c-ffc7af79a3a1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['LST1', 'AIF1', 'FCER1G', ..., 'RPL13A', 'RPL13', 'RPL3'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'NKG7' 'GZMB' ... 'RPL18A' 'RPL32'</div><input id='attrs-4a22edba-7194-4208-888f-899c16d405bf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4a22edba-7194-4208-888f-899c16d405bf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e31cd66d-1ca3-47dc-93a8-5eeec9c75ab4' class='xr-var-data-in' type='checkbox'><label for='data-e31cd66d-1ca3-47dc-93a8-5eeec9c75ab4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['NKG7', 'GZMB', 'GNLY', ..., 'RPL28', 'RPL18A', 'RPL32'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'HLA-DPA1' 'HLA-DPB1' ... 'MALAT1'</div><input id='attrs-4d05cd82-04c0-44ec-93a1-6200edd3f8ac' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4d05cd82-04c0-44ec-93a1-6200edd3f8ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5de3b3e7-3110-4152-862b-d808b2dc27f9' class='xr-var-data-in' type='checkbox'><label for='data-5de3b3e7-3110-4152-862b-d808b2dc27f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['HLA-DPA1', 'HLA-DPB1', 'HLA-DRA', ..., 'RPL21', 'RPS27', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'PF4' 'SDPR' ... 'MALAT1' 'RPL10'</div><input id='attrs-6a5fbe92-972c-42df-be67-f089659573c6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6a5fbe92-972c-42df-be67-f089659573c6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c02ae5b4-5865-4b77-b4c3-547bbccecbb1' class='xr-var-data-in' type='checkbox'><label for='data-c02ae5b4-5865-4b77-b4c3-547bbccecbb1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['PF4', 'SDPR', 'GNG11', ..., 'RPL11', 'MALAT1', 'RPL10'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f38157a3-7f97-4fa9-bbd0-5ea56377a332' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f38157a3-7f97-4fa9-bbd0-5ea56377a332' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838,\n", | |
| " PCs_1: 50, X_pca_0: 2638, X_pca_1: 50,\n", | |
| " X_umap_0: 2638, X_umap_1: 2,\n", | |
| " rank_genes_groups: 13714, genes_groups: 8)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTT...\n", | |
| " * vars (vars) object 'TNFRSF4' ... 'PRMT2'\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 ... 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 ... 13713\n", | |
| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
| "Data variables: (12/37)\n", | |
| " n_genes (obs) int64 781 1352 1131 ... 622 454 724\n", | |
| " n_genes_by_counts (obs) int32 779 1352 1129 ... 622 452 723\n", | |
| " total_counts (vars) float32 209.0 256.0 ... 207.0 745.0\n", | |
| " total_counts_mt (obs) float32 73.0 186.0 28.0 ... 21.0 16.0\n", | |
| " pct_counts_mt (obs) float32 3.018 3.794 ... 2.055 0.8065\n", | |
| " leiden (obs) object 'CD8 T' 'B' ... 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " names_B (rank_genes_groups) object 'CD74' ... 'S...\n", | |
| " names_CD8 T (rank_genes_groups) object 'CCL5' ... 'T...\n", | |
| " names_NK (rank_genes_groups) object 'LST1' ... 'R...\n", | |
| " names_FCGR3A Monocytes (rank_genes_groups) object 'NKG7' ... 'R...\n", | |
| " names_Dendritic (rank_genes_groups) object 'HLA-DPA1' .....\n", | |
| " names_Megakaryocytes (rank_genes_groups) object 'PF4' ... 'RP..." | |
| ] | |
| }, | |
| "execution_count": 19, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata_ds" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Write to Disk\n", | |
| "\n", | |
| "Once we have our XArray all setup we'll want to dump it to disk." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 20, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [], | |
| "source": [ | |
| "if os.path.exists('write/pbmc3k_ds.zarr'):\n", | |
| " adata_ds.to_zarr('write/pbmc3k_ds.zarr', mode=\"w\")\n", | |
| "else:\n", | |
| " adata_ds.to_zarr('write/pbmc3k_ds.zarr')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 21, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
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| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838,\n", | |
| " PCs_1: 50, X_pca_0: 2638, X_pca_1: 50,\n", | |
| " X_umap_0: 2638, X_umap_1: 2,\n", | |
| " rank_genes_groups: 13714, genes_groups: 8)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTT...\n", | |
| " * vars (vars) object 'TNFRSF4' ... 'PRMT2'\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 ... 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 ... 13713\n", | |
| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
| "Data variables: (12/37)\n", | |
| " n_genes (obs) int64 781 1352 1131 ... 622 454 724\n", | |
| " n_genes_by_counts (obs) int32 779 1352 1129 ... 622 452 723\n", | |
| " total_counts (vars) float32 209.0 256.0 ... 207.0 745.0\n", | |
| " total_counts_mt (obs) float32 73.0 186.0 28.0 ... 21.0 16.0\n", | |
| " pct_counts_mt (obs) float32 3.018 3.794 ... 2.055 0.8065\n", | |
| " leiden (obs) object 'CD8 T' 'B' ... 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " names_B (rank_genes_groups) object 'CD74' ... 'S...\n", | |
| " names_CD8 T (rank_genes_groups) object 'CCL5' ... 'T...\n", | |
| " names_NK (rank_genes_groups) object 'LST1' ... 'R...\n", | |
| " names_FCGR3A Monocytes (rank_genes_groups) object 'NKG7' ... 'R...\n", | |
| " names_Dendritic (rank_genes_groups) object 'HLA-DPA1' .....\n", | |
| " names_Megakaryocytes (rank_genes_groups) object 'PF4' ... 'RP...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-8c12bc90-cd1a-4c24-9dc9-ccd0af341aa4' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-8c12bc90-cd1a-4c24-9dc9-ccd0af341aa4' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>obs</span>: 2638</li><li><span class='xr-has-index'>vars</span>: 1838</li><li><span class='xr-has-index'>PCs_0</span>: 1838</li><li><span class='xr-has-index'>PCs_1</span>: 50</li><li><span class='xr-has-index'>X_pca_0</span>: 2638</li><li><span class='xr-has-index'>X_pca_1</span>: 50</li><li><span class='xr-has-index'>X_umap_0</span>: 2638</li><li><span class='xr-has-index'>X_umap_1</span>: 2</li><li><span class='xr-has-index'>rank_genes_groups</span>: 13714</li><li><span class='xr-has-index'>genes_groups</span>: 8</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-a308bf7a-2fca-41d9-960f-ec1ff06eb28d' class='xr-section-summary-in' type='checkbox' checked><label for='section-a308bf7a-2fca-41d9-960f-ec1ff06eb28d' class='xr-section-summary' >Coordinates: <span>(10)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>obs</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'AAACATACAACCAC-1' ... 'TTTGCATG...</div><input id='attrs-1d9b2306-fc1d-43ee-9ecd-bab39af4d76a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1d9b2306-fc1d-43ee-9ecd-bab39af4d76a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-03bba595-36b4-4cf9-be7e-79cbdb2d93f8' class='xr-var-data-in' type='checkbox'><label for='data-03bba595-36b4-4cf9-be7e-79cbdb2d93f8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1', ...,\n", | |
| " 'TTTCTACTTCCTCG-1', 'TTTGCATGAGAGGC-1', 'TTTGCATGCCTCAC-1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>vars</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'TNFRSF4' 'CPSF3L' ... 'PRMT2'</div><input id='attrs-217e54ea-f432-4f93-b4e5-a8bfbcf947cf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-217e54ea-f432-4f93-b4e5-a8bfbcf947cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ffe22607-2ba1-4ebc-92ce-8a67f17df6f1' class='xr-var-data-in' type='checkbox'><label for='data-ffe22607-2ba1-4ebc-92ce-8a67f17df6f1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['TNFRSF4', 'CPSF3L', 'ATAD3C', ..., 'SLC19A1', 'S100B', 'PRMT2'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_0</span></div><div class='xr-var-dims'>(PCs_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 1834 1835 1836 1837</div><input id='attrs-b19c2dca-7278-4c8f-95dc-d1b8e3956e7d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b19c2dca-7278-4c8f-95dc-d1b8e3956e7d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d063a674-3ccd-4679-9536-dcb230a2d8f4' class='xr-var-data-in' type='checkbox'><label for='data-d063a674-3ccd-4679-9536-dcb230a2d8f4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 1835, 1836, 1837])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_1</span></div><div class='xr-var-dims'>(PCs_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-0211ad1f-d4ab-4392-92e3-4113e0cae16a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0211ad1f-d4ab-4392-92e3-4113e0cae16a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19a3c1e8-1095-4c66-8c6d-95859a517f14' class='xr-var-data-in' type='checkbox'><label for='data-19a3c1e8-1095-4c66-8c6d-95859a517f14' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_0</span></div><div class='xr-var-dims'>(X_pca_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-ade82fea-e820-46b2-9b3d-c75082fae441' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ade82fea-e820-46b2-9b3d-c75082fae441' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-13286b58-d11f-472b-b6a0-a02486b74769' class='xr-var-data-in' type='checkbox'><label for='data-13286b58-d11f-472b-b6a0-a02486b74769' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_1</span></div><div class='xr-var-dims'>(X_pca_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-640162a8-d998-47ed-b070-9cedee667414' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-640162a8-d998-47ed-b070-9cedee667414' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2454475c-6005-4bcf-8157-6b58e9cd6cb5' class='xr-var-data-in' type='checkbox'><label for='data-2454475c-6005-4bcf-8157-6b58e9cd6cb5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_0</span></div><div class='xr-var-dims'>(X_umap_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-73959a04-f1bf-40f1-8d83-b405110fbbf4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-73959a04-f1bf-40f1-8d83-b405110fbbf4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8a5dc10-07fa-43d6-96c7-cef76f33e1a9' class='xr-var-data-in' type='checkbox'><label for='data-b8a5dc10-07fa-43d6-96c7-cef76f33e1a9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_1</span></div><div class='xr-var-dims'>(X_umap_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1</div><input id='attrs-11d57848-649c-4470-ba40-af9394073d47' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-11d57848-649c-4470-ba40-af9394073d47' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c8478c24-7398-42ed-82f8-ab4f694c2f38' class='xr-var-data-in' type='checkbox'><label for='data-c8478c24-7398-42ed-82f8-ab4f694c2f38' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0, 1])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>rank_genes_groups</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 ... 13710 13711 13712 13713</div><input id='attrs-350541e4-edd5-48ab-9a05-1aa44e3be614' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-350541e4-edd5-48ab-9a05-1aa44e3be614' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1a01f6b5-3b57-4595-a81d-e58b88bfe2e5' class='xr-var-data-in' type='checkbox'><label for='data-1a01f6b5-3b57-4595-a81d-e58b88bfe2e5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 13711, 13712, 13713])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genes_groups</span></div><div class='xr-var-dims'>(genes_groups)</div><div class='xr-var-dtype'><U16</div><div class='xr-var-preview xr-preview'>'CD4 T' ... 'Megakaryocytes'</div><input id='attrs-158d07e5-eb85-4a9e-877a-ba3e1dc71181' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-158d07e5-eb85-4a9e-877a-ba3e1dc71181' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5f53fc8a-0f41-4c5e-a95f-f3c015bc3354' class='xr-var-data-in' type='checkbox'><label for='data-5f53fc8a-0f41-4c5e-a95f-f3c015bc3354' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD4 T', 'CD14 Monocytes', 'B', 'CD8 T', 'NK', 'FCGR3A Monocytes',\n", | |
| " 'Dendritic', 'Megakaryocytes'], dtype='<U16')</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-556f4e78-e07a-4a37-a447-cfcd672146a9' class='xr-section-summary-in' type='checkbox' ><label for='section-556f4e78-e07a-4a37-a447-cfcd672146a9' class='xr-section-summary' >Data variables: <span>(37)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>n_genes</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>781 1352 1131 960 ... 622 454 724</div><input id='attrs-7272256f-039e-4d0e-9e7c-e59227ac5bec' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7272256f-039e-4d0e-9e7c-e59227ac5bec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-201ab1a4-2fbf-4c1a-b431-1de5e5493ed4' class='xr-var-data-in' type='checkbox'><label for='data-201ab1a4-2fbf-4c1a-b431-1de5e5493ed4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 781, 1352, 1131, ..., 622, 454, 724])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_genes_by_counts</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>779 1352 1129 960 ... 622 452 723</div><input id='attrs-ff0de293-456e-48ae-89ef-9c28418f3e0a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ff0de293-456e-48ae-89ef-9c28418f3e0a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bdf174bf-647a-4d60-906e-83a378de033c' class='xr-var-data-in' type='checkbox'><label for='data-bdf174bf-647a-4d60-906e-83a378de033c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 779, 1352, 1129, ..., 622, 452, 723], dtype=int32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>209.0 256.0 25.0 ... 207.0 745.0</div><input id='attrs-0aee4ab9-f546-4583-9f5c-eb4e10ab788b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0aee4ab9-f546-4583-9f5c-eb4e10ab788b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a50b390c-b93c-4d62-aacf-8740bd522db8' class='xr-var-data-in' type='checkbox'><label for='data-a50b390c-b93c-4d62-aacf-8740bd522db8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([209., 256., 25., ..., 50., 207., 745.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>total_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>73.0 186.0 28.0 ... 37.0 21.0 16.0</div><input id='attrs-23f18b28-1743-490c-9dee-5ee7182dc604' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-23f18b28-1743-490c-9dee-5ee7182dc604' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6b01685a-9335-4018-8a5c-e46834402dd3' class='xr-var-data-in' type='checkbox'><label for='data-6b01685a-9335-4018-8a5c-e46834402dd3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 73., 186., 28., ..., 37., 21., 16.], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>3.018 3.794 0.8897 ... 2.055 0.8065</div><input id='attrs-38484d7d-3754-4f25-8dd3-7e162ec382c4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-38484d7d-3754-4f25-8dd3-7e162ec382c4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0c8d0415-78fb-418f-8ade-f502a13c99b5' class='xr-var-data-in' type='checkbox'><label for='data-0c8d0415-78fb-418f-8ade-f502a13c99b5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([3.017776 , 3.7935958 , 0.88973624, ..., 2.1971495 , 2.0547945 ,\n", | |
| " 0.80645156], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>leiden</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD8 T' 'B' 'CD4 T' ... 'B' 'CD4 T'</div><input id='attrs-c748ad64-4aa9-4f2a-92ee-e2e636796395' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c748ad64-4aa9-4f2a-92ee-e2e636796395' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1684f944-1485-462e-a528-995ae4ea4034' class='xr-var-data-in' type='checkbox'><label for='data-1684f944-1485-462e-a528-995ae4ea4034' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD8 T', 'B', 'CD4 T', ..., 'B', 'B', 'CD4 T'], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>gene_ids</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'ENSG00000186827' ... 'ENSG00000...</div><input id='attrs-3ab510f5-b6ff-4405-a998-3154b8f2885c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3ab510f5-b6ff-4405-a998-3154b8f2885c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-46722353-ee3b-45a1-a0ec-401c5a7cf14c' class='xr-var-data-in' type='checkbox'><label for='data-46722353-ee3b-45a1-a0ec-401c5a7cf14c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['ENSG00000186827', 'ENSG00000127054', 'ENSG00000215915', ...,\n", | |
| " 'ENSG00000173638', 'ENSG00000160307', 'ENSG00000160310'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-bddb3eaf-b498-4d77-838c-53a5ca4ebbf1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bddb3eaf-b498-4d77-838c-53a5ca4ebbf1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ce3f5117-3489-4778-bbe5-9847c1992722' class='xr-var-data-in' type='checkbox'><label for='data-ce3f5117-3489-4778-bbe5-9847c1992722' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mt</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... False False</div><input id='attrs-fb0f05a1-7c91-4a59-b6e6-9efcad84affc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb0f05a1-7c91-4a59-b6e6-9efcad84affc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1de3f885-382a-4dda-9444-8d2681fa5a2a' class='xr-var-data-in' type='checkbox'><label for='data-1de3f885-382a-4dda-9444-8d2681fa5a2a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, ..., False, False, False])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>155 202 9 501 608 ... 570 31 94 588</div><input id='attrs-bf1f4895-e45d-4953-9e6a-8855b7c20cad' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bf1f4895-e45d-4953-9e6a-8855b7c20cad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a93186e9-4584-4126-bec9-860808aee8d3' class='xr-var-data-in' type='checkbox'><label for='data-a93186e9-4584-4126-bec9-860808aee8d3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([155, 202, 9, ..., 31, 94, 588])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.07741 0.09481 ... 0.07667 0.2759</div><input id='attrs-9b6a1fc8-eb57-40b8-8d43-74236e07c352' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9b6a1fc8-eb57-40b8-8d43-74236e07c352' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d3c87407-17b0-4563-9147-5438dd2b9ffe' class='xr-var-data-in' type='checkbox'><label for='data-d3c87407-17b0-4563-9147-5438dd2b9ffe' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.0774074 , 0.09481481, 0.00925926, ..., 0.01851852, 0.07666667,\n", | |
| " 0.27592593], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_dropout_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>94.26 92.52 99.67 ... 96.52 78.22</div><input id='attrs-66e45270-6154-4f0a-afcf-8d93ce22ca6a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-66e45270-6154-4f0a-afcf-8d93ce22ca6a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-167c574c-1bb8-4a3e-85a5-cca23a5a60d2' class='xr-var-data-in' type='checkbox'><label for='data-167c574c-1bb8-4a3e-85a5-cca23a5a60d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([94.25925926, 92.51851852, 99.66666667, ..., 98.85185185,\n", | |
| " 96.51851852, 78.22222222])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>highly_variable</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>True True True ... True True True</div><input id='attrs-6be16218-7bec-4b2d-8eca-cd829c1ad759' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6be16218-7bec-4b2d-8eca-cd829c1ad759' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fd21b027-a411-4099-9676-a2cfd242f689' class='xr-var-data-in' type='checkbox'><label for='data-fd21b027-a411-4099-9676-a2cfd242f689' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ True, True, True, ..., True, True, True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>means</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.2774 0.3852 ... 0.2863 0.8166</div><input id='attrs-835e0740-171f-451d-9037-cf58f058b2f7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-835e0740-171f-451d-9037-cf58f058b2f7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e9e656f3-7ead-41a9-a2f4-4f0b645c1ca7' class='xr-var-data-in' type='checkbox'><label for='data-e9e656f3-7ead-41a9-a2f4-4f0b645c1ca7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.27741027, 0.38519408, 0.03825194, ..., 0.05895963, 0.28628215,\n", | |
| " 0.81664652])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>2.086 4.507 3.953 ... 3.043 2.774</div><input id='attrs-565e3af4-ac04-43bb-97f7-ca445cf9fcb1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-565e3af4-ac04-43bb-97f7-ca445cf9fcb1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b9aa4519-e81b-4975-8163-ac5d812ee851' class='xr-var-data-in' type='checkbox'><label for='data-b9aa4519-e81b-4975-8163-ac5d812ee851' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([2.08604962, 4.5069874 , 3.95348633, ..., 3.23423114, 3.04299217,\n", | |
| " 2.77416884])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions_norm</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>0.6654 2.955 4.353 ... 1.079 0.6291</div><input id='attrs-dda344ff-0ac7-4126-9443-d7e86e6d7903' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dda344ff-0ac7-4126-9443-d7e86e6d7903' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fce9aa85-9011-4487-9a45-53264c0eab3e' class='xr-var-data-in' type='checkbox'><label for='data-fce9aa85-9011-4487-9a45-53264c0eab3e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.66540575, 2.955005 , 4.3526073 , ..., 2.9324582 , 1.0787829 ,\n", | |
| " 0.62905824], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>-3.672e-10 ... -6.101e-10</div><input id='attrs-5b425ed7-4816-473d-8853-6035434a1d4a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5b425ed7-4816-473d-8853-6035434a1d4a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-609daa4f-3e05-4574-b913-86328085b551' class='xr-var-data-in' type='checkbox'><label for='data-609daa4f-3e05-4574-b913-86328085b551' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([-3.67206934e-10, -2.37243658e-10, 8.47298779e-12, ...,\n", | |
| " -2.02096928e-10, 5.99463886e-10, -6.10055121e-10])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>std</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.4245 0.4604 ... 0.3999 0.7628</div><input id='attrs-8ff73125-1a36-4804-a76b-265e69590dfa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8ff73125-1a36-4804-a76b-265e69590dfa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6f23842e-50d9-407b-8ff8-a005b3fd00d5' class='xr-var-data-in' type='checkbox'><label for='data-6f23842e-50d9-407b-8ff8-a005b3fd00d5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0.42448087, 0.46041616, 0.11946545, ..., 0.17301715, 0.39994584,\n", | |
| " 0.7627529 ])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PCs</span></div><div class='xr-var-dims'>(PCs_0, PCs_1)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838, 50), meta=np.ndarray></div><input id='attrs-29581ab5-f6b1-4ec9-ad74-27f44ea59d9d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-29581ab5-f6b1-4ec9-ad74-27f44ea59d9d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-da2b5e9c-8928-4ef2-a5b6-0a951a76edbf' class='xr-var-data-in' type='checkbox'><label for='data-da2b5e9c-8928-4ef2-a5b6-0a951a76edbf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"80\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"30\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"30\" y1=\"0\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 30.80809411591093,0.0 30.80809411591093,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"15.404047\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"50.808094\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,50.808094,60.000000)\">1838</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_pca</span></div><div class='xr-var-dims'>(X_pca_0, X_pca_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 50), meta=np.ndarray></div><input id='attrs-73fed2aa-fc59-4efe-a7a6-3f7725e77818' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-73fed2aa-fc59-4efe-a7a6-3f7725e77818' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4b74918c-062d-4dd6-a881-329a886662d3' class='xr-var-data-in' type='checkbox'><label for='data-4b74918c-062d-4dd6-a881-329a886662d3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"78\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"28\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"28\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"28\" y1=\"0\" x2=\"28\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 28.72981340784082,0.0 28.72981340784082,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"14.364907\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"48.729813\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,48.729813,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_umap</span></div><div class='xr-var-dims'>(X_umap_0, X_umap_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 2), meta=np.ndarray></div><input id='attrs-cbfa76a3-4623-43ba-95e3-3ac3fed4196b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cbfa76a3-4623-43ba-95e3-3ac3fed4196b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-de87fa02-082c-49ab-8e4a-7c7c5fa90448' class='xr-var-data-in' type='checkbox'><label for='data-de87fa02-082c-49ab-8e4a-7c7c5fa90448' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 1 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"75\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 25.412616514582485,0.0 25.412616514582485,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"12.706308\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >2</text>\n", | |
| " <text x=\"45.412617\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,45.412617,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>1.042 2.668 1.165 ... -2.076 -2.819</div><input id='attrs-ffbcdd91-082f-4cb0-8df7-b12b20996df7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ffbcdd91-082f-4cb0-8df7-b12b20996df7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-224dbb82-5a28-4405-992b-9ea3fe038688' class='xr-var-data-in' type='checkbox'><label for='data-224dbb82-5a28-4405-992b-9ea3fe038688' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 1.0415391, 2.6682508, 1.1648842, ..., -4.3634076, -2.075822 ,\n", | |
| " -2.818502 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>7.36 6.167 7.483 ... -2.032 -1.598</div><input id='attrs-bf16d0e3-428d-4147-8507-66d408bf32da' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bf16d0e3-428d-4147-8507-66d408bf32da' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-79932569-5289-4077-a42a-ed99d173792c' class='xr-var-data-in' type='checkbox'><label for='data-79932569-5289-4077-a42a-ed99d173792c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 7.3599567, 6.1667976, 7.4828935, ..., -1.2195065, -2.0324383,\n", | |
| " -1.5976202], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.08 7.75 4.887 ... -0.8629 -3.911</div><input id='attrs-defec71e-4b4b-422c-862d-7a843a5e5b78' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-defec71e-4b4b-422c-862d-7a843a5e5b78' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23f6e395-f7e0-4a90-9858-40024618f6d9' class='xr-var-data-in' type='checkbox'><label for='data-23f6e395-f7e0-4a90-9858-40024618f6d9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.0795345, 7.749746 , 4.8870344, ..., -3.1592414, -0.8628794,\n", | |
| " -3.9112678], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.322 4.926 ... -0.7609 -0.6679</div><input id='attrs-78ae24c2-f38c-4319-8202-68d5e03f7508' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-78ae24c2-f38c-4319-8202-68d5e03f7508' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-91097c47-689b-4dfe-9021-79ec1fb5ca74' class='xr-var-data-in' type='checkbox'><label for='data-91097c47-689b-4dfe-9021-79ec1fb5ca74' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.3217707 , 4.9258666 , 0.76513237, ..., -1.080934 ,\n", | |
| " -0.7609468 , -0.6679198 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>5.141 4.887 4.791 ... -1.013 -1.202</div><input id='attrs-78003d17-830b-4ccd-8e8f-7d5058371549' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-78003d17-830b-4ccd-8e8f-7d5058371549' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a2adb18a-743c-4c18-80bb-20404364ad20' class='xr-var-data-in' type='checkbox'><label for='data-a2adb18a-743c-4c18-80bb-20404364ad20' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 5.141453 , 4.8865533 , 4.791256 , ..., -0.97208005,\n", | |
| " -1.0129575 , -1.2016066 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>6.869 7.695 7.759 ... -1.337 -1.286</div><input id='attrs-4e713167-779b-4f3d-896a-b15835a38d59' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4e713167-779b-4f3d-896a-b15835a38d59' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-56cdec80-127b-42d7-a170-d00f37604252' class='xr-var-data-in' type='checkbox'><label for='data-56cdec80-127b-42d7-a170-d00f37604252' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 6.8688717, 7.6950693, 7.759242 , ..., -1.0524981, -1.33682 ,\n", | |
| " -1.2857121], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>4.278 4.435 ... -0.7723 -1.179</div><input id='attrs-63722571-8403-4f07-b87e-f2403d94ee16' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-63722571-8403-4f07-b87e-f2403d94ee16' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-77440ad4-f46c-4244-9f8f-6ae08ae1369e' class='xr-var-data-in' type='checkbox'><label for='data-77440ad4-f46c-4244-9f8f-6ae08ae1369e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 4.2783146 , 4.4348464 , 4.6085496 , ..., -0.7930738 ,\n", | |
| " -0.77232665, -1.1790817 ], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>12.91 11.86 12.43 ... -3.965 -4.84</div><input id='attrs-3d258309-8c6a-474a-b1ca-4a13ec342c6a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3d258309-8c6a-474a-b1ca-4a13ec342c6a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-50e2e34a-866f-4546-b192-758ff8ac2420' class='xr-var-data-in' type='checkbox'><label for='data-50e2e34a-866f-4546-b192-758ff8ac2420' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([12.905741 , 11.863666 , 12.428451 , ..., -5.350221 , -3.9652784,\n", | |
| " -4.8402567], dtype=float32)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'RPS12' 'LDHB' ... 'CYBA' 'CD74'</div><input id='attrs-aaaaf195-7a36-488c-966e-76d1a347bda5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aaaaf195-7a36-488c-966e-76d1a347bda5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2de59ea2-deac-4162-9b23-8cb19fbb3efa' class='xr-var-data-in' type='checkbox'><label for='data-2de59ea2-deac-4162-9b23-8cb19fbb3efa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['RPS12', 'LDHB', 'RPS25', ..., 'HLA-DRA', 'CYBA', 'CD74'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'S100A9' 'LYZ' ... 'MALAT1'</div><input id='attrs-cd3cb3b7-f544-4a78-8da1-09c445419f65' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cd3cb3b7-f544-4a78-8da1-09c445419f65' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e039cd6e-78d8-4f9a-84ed-112c837f6bc9' class='xr-var-data-in' type='checkbox'><label for='data-e039cd6e-78d8-4f9a-84ed-112c837f6bc9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['S100A9', 'LYZ', 'S100A8', ..., 'RPS27', 'RPS27A', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CD74' 'CD79A' ... 'S100A4'</div><input id='attrs-5ba59d99-9fd3-44df-a938-b165730a2bb8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5ba59d99-9fd3-44df-a938-b165730a2bb8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-522f763f-1332-447d-a41b-1ac867098615' class='xr-var-data-in' type='checkbox'><label for='data-522f763f-1332-447d-a41b-1ac867098615' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD74', 'CD79A', 'HLA-DRA', ..., 'S100A6', 'TMSB4X', 'S100A4'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'CCL5' 'NKG7' ... 'RPS11' 'TMSB10'</div><input id='attrs-68585a65-f9c4-4b62-85c1-081cd052a39d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-68585a65-f9c4-4b62-85c1-081cd052a39d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0cf390fb-8072-4408-8b0e-e71975bf6301' class='xr-var-data-in' type='checkbox'><label for='data-0cf390fb-8072-4408-8b0e-e71975bf6301' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CCL5', 'NKG7', 'B2M', ..., 'FTH1', 'RPS11', 'TMSB10'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'LST1' 'AIF1' ... 'RPL13' 'RPL3'</div><input id='attrs-cd094629-6fb9-42f5-a35d-d7ae44dfe084' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cd094629-6fb9-42f5-a35d-d7ae44dfe084' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e47acacc-eae8-4b20-ad4b-6928ab51b853' class='xr-var-data-in' type='checkbox'><label for='data-e47acacc-eae8-4b20-ad4b-6928ab51b853' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['LST1', 'AIF1', 'FCER1G', ..., 'RPL13A', 'RPL13', 'RPL3'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'NKG7' 'GZMB' ... 'RPL18A' 'RPL32'</div><input id='attrs-823b723e-3f80-4318-9caa-5d14c2294f84' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-823b723e-3f80-4318-9caa-5d14c2294f84' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-88981f2e-daaf-4187-8d40-2502c62b448d' class='xr-var-data-in' type='checkbox'><label for='data-88981f2e-daaf-4187-8d40-2502c62b448d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['NKG7', 'GZMB', 'GNLY', ..., 'RPL28', 'RPL18A', 'RPL32'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'HLA-DPA1' 'HLA-DPB1' ... 'MALAT1'</div><input id='attrs-688e7b13-b421-4b79-b1ba-1723e1333545' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-688e7b13-b421-4b79-b1ba-1723e1333545' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c9eba56-d5cb-4677-a726-ec8260209629' class='xr-var-data-in' type='checkbox'><label for='data-1c9eba56-d5cb-4677-a726-ec8260209629' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['HLA-DPA1', 'HLA-DPB1', 'HLA-DRA', ..., 'RPL21', 'RPS27', 'MALAT1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'PF4' 'SDPR' ... 'MALAT1' 'RPL10'</div><input id='attrs-da903cde-1177-4036-9647-9b67ea1146e1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da903cde-1177-4036-9647-9b67ea1146e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bcda4551-8b4b-47d3-9ca5-009aa1d742e6' class='xr-var-data-in' type='checkbox'><label for='data-bcda4551-8b4b-47d3-9ca5-009aa1d742e6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['PF4', 'SDPR', 'GNG11', ..., 'RPL11', 'MALAT1', 'RPL10'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b6d0f4f3-eece-4819-99b8-9025b49de764' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b6d0f4f3-eece-4819-99b8-9025b49de764' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (obs: 2638, vars: 1838, PCs_0: 1838,\n", | |
| " PCs_1: 50, X_pca_0: 2638, X_pca_1: 50,\n", | |
| " X_umap_0: 2638, X_umap_1: 2,\n", | |
| " rank_genes_groups: 13714, genes_groups: 8)\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTT...\n", | |
| " * vars (vars) object 'TNFRSF4' ... 'PRMT2'\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 ... 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 ... 13713\n", | |
| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
| "Data variables: (12/37)\n", | |
| " n_genes (obs) int64 781 1352 1131 ... 622 454 724\n", | |
| " n_genes_by_counts (obs) int32 779 1352 1129 ... 622 452 723\n", | |
| " total_counts (vars) float32 209.0 256.0 ... 207.0 745.0\n", | |
| " total_counts_mt (obs) float32 73.0 186.0 28.0 ... 21.0 16.0\n", | |
| " pct_counts_mt (obs) float32 3.018 3.794 ... 2.055 0.8065\n", | |
| " leiden (obs) object 'CD8 T' 'B' ... 'B' 'CD4 T'\n", | |
| " ... ...\n", | |
| " names_B (rank_genes_groups) object 'CD74' ... 'S...\n", | |
| " names_CD8 T (rank_genes_groups) object 'CCL5' ... 'T...\n", | |
| " names_NK (rank_genes_groups) object 'LST1' ... 'R...\n", | |
| " names_FCGR3A Monocytes (rank_genes_groups) object 'NKG7' ... 'R...\n", | |
| " names_Dendritic (rank_genes_groups) object 'HLA-DPA1' .....\n", | |
| " names_Megakaryocytes (rank_genes_groups) object 'PF4' ... 'RP..." | |
| ] | |
| }, | |
| "execution_count": 21, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
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| "source": [ | |
| "adata_ds" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 22, | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%%\n" | |
| } | |
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| "outputs": [ | |
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| "</style><pre class='xr-text-repr-fallback'><xarray.DataArray 'n_genes' (obs: 2638)>\n", | |
| "array([ 781, 1352, 1131, ..., 622, 454, 724])\n", | |
| "Coordinates:\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTTGCATGCCTCAC-1'</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'n_genes'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>obs</span>: 2638</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-450a848f-f120-43fd-9274-39ccff10d09c' class='xr-array-in' type='checkbox' checked><label for='section-450a848f-f120-43fd-9274-39ccff10d09c' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>781 1352 1131 960 522 782 783 790 ... 873 1544 1155 1227 622 454 724</span></div><div class='xr-array-data'><pre>array([ 781, 1352, 1131, ..., 622, 454, 724])</pre></div></div></li><li class='xr-section-item'><input id='section-d29580bb-34a9-4351-be76-1e4eca4cb751' class='xr-section-summary-in' type='checkbox' checked><label for='section-d29580bb-34a9-4351-be76-1e4eca4cb751' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>obs</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'AAACATACAACCAC-1' ... 'TTTGCATG...</div><input id='attrs-813ea80f-0cf4-42ab-a04a-b0cbfed29281' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-813ea80f-0cf4-42ab-a04a-b0cbfed29281' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f0b46bf7-81a7-43e9-80d7-47de68ea56ef' class='xr-var-data-in' type='checkbox'><label for='data-f0b46bf7-81a7-43e9-80d7-47de68ea56ef' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1', ...,\n", | |
| " 'TTTCTACTTCCTCG-1', 'TTTGCATGAGAGGC-1', 'TTTGCATGCCTCAC-1'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f81bb24e-512e-44b9-bd34-c6bcb7d8a27a' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f81bb24e-512e-44b9-bd34-c6bcb7d8a27a' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
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| "## Read the XArray Dataset \n", | |
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| "adata_ds_zarr = xr.open_zarr('write/pbmc3k_ds.zarr')" | |
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| "\n", | |
| ".xr-array-in:checked ~ .xr-array-data,\n", | |
| ".xr-array-preview {\n", | |
| " display: inline-block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list {\n", | |
| " display: inline-block !important;\n", | |
| " list-style: none;\n", | |
| " padding: 0 !important;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li {\n", | |
| " display: inline-block;\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:before {\n", | |
| " content: '(';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:after {\n", | |
| " content: ')';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li:not(:last-child):after {\n", | |
| " content: ',';\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-has-index {\n", | |
| " font-weight: bold;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list,\n", | |
| ".xr-var-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > div,\n", | |
| ".xr-var-item label,\n", | |
| ".xr-var-item > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-even);\n", | |
| " margin-bottom: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-odd);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name {\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dims {\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dtype {\n", | |
| " grid-column: 3;\n", | |
| " text-align: right;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-preview {\n", | |
| " grid-column: 4;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name,\n", | |
| ".xr-var-dims,\n", | |
| ".xr-var-dtype,\n", | |
| ".xr-preview,\n", | |
| ".xr-attrs dt {\n", | |
| " white-space: nowrap;\n", | |
| " overflow: hidden;\n", | |
| " text-overflow: ellipsis;\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name:hover,\n", | |
| ".xr-var-dims:hover,\n", | |
| ".xr-var-dtype:hover,\n", | |
| ".xr-attrs dt:hover {\n", | |
| " overflow: visible;\n", | |
| " width: auto;\n", | |
| " z-index: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " display: none;\n", | |
| " background-color: var(--xr-background-color) !important;\n", | |
| " padding-bottom: 5px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", | |
| ".xr-var-data-in:checked ~ .xr-var-data {\n", | |
| " display: block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-data > table {\n", | |
| " float: right;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name span,\n", | |
| ".xr-var-data,\n", | |
| ".xr-attrs {\n", | |
| " padding-left: 25px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs,\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " grid-column: 1 / -1;\n", | |
| "}\n", | |
| "\n", | |
| "dl.xr-attrs {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 125px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt,\n", | |
| ".xr-attrs dd {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (PCs_0: 1838, PCs_1: 50, X_pca_0: 2638,\n", | |
| " X_pca_1: 50, X_umap_0: 2638, X_umap_1: 2,\n", | |
| " vars: 1838, genes_groups: 8, obs: 2638,\n", | |
| " rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 ... 46 47 48 49\n", | |
| " * X_umap_0 (X_umap_0) int64 0 1 2 3 ... 2635 2636 2637\n", | |
| " * X_umap_1 (X_umap_1) int64 0 1\n", | |
| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
| " * obs (obs) object 'AAACATACAACCAC-1' ... 'TTT...\n", | |
| " * rank_genes_groups (rank_genes_groups) int64 0 1 ... 13713\n", | |
| " * vars (vars) object 'TNFRSF4' ... 'PRMT2'\n", | |
| "Data variables: (12/37)\n", | |
| " PCs (PCs_0, PCs_1) float64 dask.array<chunksize=(1838, 50), meta=np.ndarray>\n", | |
| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray>\n", | |
| " X_umap (X_umap_0, X_umap_1) float32 dask.array<chunksize=(2638, 2), meta=np.ndarray>\n", | |
| " dispersions (vars) float64 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " dispersions_norm (vars) float32 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " gene_ids (vars) object dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " ... ...\n", | |
| " names_NK (rank_genes_groups) object dask.array<chunksize=(13714,), meta=np.ndarray>\n", | |
| " pct_counts_mt (obs) float32 dask.array<chunksize=(2638,), meta=np.ndarray>\n", | |
| " pct_dropout_by_counts (vars) float64 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " std (vars) float64 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " total_counts (vars) float32 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " total_counts_mt (obs) float32 dask.array<chunksize=(2638,), meta=np.ndarray></pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-acf42cfd-fe67-49f3-bc22-912ccfc8a1c2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-acf42cfd-fe67-49f3-bc22-912ccfc8a1c2' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>PCs_0</span>: 1838</li><li><span class='xr-has-index'>PCs_1</span>: 50</li><li><span class='xr-has-index'>X_pca_0</span>: 2638</li><li><span class='xr-has-index'>X_pca_1</span>: 50</li><li><span class='xr-has-index'>X_umap_0</span>: 2638</li><li><span class='xr-has-index'>X_umap_1</span>: 2</li><li><span class='xr-has-index'>vars</span>: 1838</li><li><span class='xr-has-index'>genes_groups</span>: 8</li><li><span class='xr-has-index'>obs</span>: 2638</li><li><span class='xr-has-index'>rank_genes_groups</span>: 13714</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-f50cbf52-5f25-4fc1-9cc2-e909e02311a6' class='xr-section-summary-in' type='checkbox' checked><label for='section-f50cbf52-5f25-4fc1-9cc2-e909e02311a6' class='xr-section-summary' >Coordinates: <span>(10)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_0</span></div><div class='xr-var-dims'>(PCs_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 1834 1835 1836 1837</div><input id='attrs-3e163e24-6c10-4967-9cb9-ee680dcd3f4b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3e163e24-6c10-4967-9cb9-ee680dcd3f4b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fee9297d-0f1c-4c9b-940d-52872265dd51' class='xr-var-data-in' type='checkbox'><label for='data-fee9297d-0f1c-4c9b-940d-52872265dd51' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 1835, 1836, 1837])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>PCs_1</span></div><div class='xr-var-dims'>(PCs_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-98f9ab92-650e-4fa1-b2f3-b92390e5904d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-98f9ab92-650e-4fa1-b2f3-b92390e5904d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e45c7844-0c69-4dd9-8e27-4eae9bdfa9c5' class='xr-var-data-in' type='checkbox'><label for='data-e45c7844-0c69-4dd9-8e27-4eae9bdfa9c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_0</span></div><div class='xr-var-dims'>(X_pca_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-e5b80fec-bc2e-497c-b43a-b2dc3976e165' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e5b80fec-bc2e-497c-b43a-b2dc3976e165' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-270b4932-ddca-4225-9747-325cc9b5c2fa' class='xr-var-data-in' type='checkbox'><label for='data-270b4932-ddca-4225-9747-325cc9b5c2fa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_1</span></div><div class='xr-var-dims'>(X_pca_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-e1234dbd-0c01-474d-8929-9e1069b0a51f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e1234dbd-0c01-474d-8929-9e1069b0a51f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62a47f9e-04b1-4a79-a56f-3e95b4cbea36' class='xr-var-data-in' type='checkbox'><label for='data-62a47f9e-04b1-4a79-a56f-3e95b4cbea36' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_0</span></div><div class='xr-var-dims'>(X_umap_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-f468e887-9cbe-4100-850e-73843daccfcc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f468e887-9cbe-4100-850e-73843daccfcc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d68d009-1b32-40d6-aa0b-f28b99fd0085' class='xr-var-data-in' type='checkbox'><label for='data-6d68d009-1b32-40d6-aa0b-f28b99fd0085' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_umap_1</span></div><div class='xr-var-dims'>(X_umap_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1</div><input id='attrs-296bfac2-24b5-47bb-b73f-8cc4ed3d039b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-296bfac2-24b5-47bb-b73f-8cc4ed3d039b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d33c775a-4e53-4849-962e-52da1a685b55' class='xr-var-data-in' type='checkbox'><label for='data-d33c775a-4e53-4849-962e-52da1a685b55' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0, 1])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genes_groups</span></div><div class='xr-var-dims'>(genes_groups)</div><div class='xr-var-dtype'><U16</div><div class='xr-var-preview xr-preview'>'CD4 T' ... 'Megakaryocytes'</div><input id='attrs-bcbeebd8-5c7d-4f40-801b-dc47173c842e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bcbeebd8-5c7d-4f40-801b-dc47173c842e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d07bd128-df24-4377-ab25-ee2b0d8cf542' class='xr-var-data-in' type='checkbox'><label for='data-d07bd128-df24-4377-ab25-ee2b0d8cf542' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['CD4 T', 'CD14 Monocytes', 'B', 'CD8 T', 'NK', 'FCGR3A Monocytes',\n", | |
| " 'Dendritic', 'Megakaryocytes'], dtype='<U16')</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>obs</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'AAACATACAACCAC-1' ... 'TTTGCATG...</div><input id='attrs-edde2e4e-d239-46b2-b337-b26a0bdcb6eb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-edde2e4e-d239-46b2-b337-b26a0bdcb6eb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-df411062-bd1d-4331-b127-8c25a7255dd3' class='xr-var-data-in' type='checkbox'><label for='data-df411062-bd1d-4331-b127-8c25a7255dd3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['AAACATACAACCAC-1', 'AAACATTGAGCTAC-1', 'AAACATTGATCAGC-1', ...,\n", | |
| " 'TTTCTACTTCCTCG-1', 'TTTGCATGAGAGGC-1', 'TTTGCATGCCTCAC-1'],\n", | |
| " dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>rank_genes_groups</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 ... 13710 13711 13712 13713</div><input id='attrs-0b76681f-57da-4c58-84c6-998c7c48d09c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0b76681f-57da-4c58-84c6-998c7c48d09c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-53b870f6-ca22-4f3e-b3a0-d0b2ad8a35fd' class='xr-var-data-in' type='checkbox'><label for='data-53b870f6-ca22-4f3e-b3a0-d0b2ad8a35fd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 13711, 13712, 13713])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>vars</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'TNFRSF4' 'CPSF3L' ... 'PRMT2'</div><input id='attrs-d91ba173-2830-4588-94aa-0172126e31b1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d91ba173-2830-4588-94aa-0172126e31b1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4caeedcd-7f60-4bcc-8ab3-f4b83d00d292' class='xr-var-data-in' type='checkbox'><label for='data-4caeedcd-7f60-4bcc-8ab3-f4b83d00d292' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['TNFRSF4', 'CPSF3L', 'ATAD3C', ..., 'SLC19A1', 'S100B', 'PRMT2'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-534ca826-5777-44a7-b26a-46b4d6443117' class='xr-section-summary-in' type='checkbox' ><label for='section-534ca826-5777-44a7-b26a-46b4d6443117' class='xr-section-summary' >Data variables: <span>(37)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>PCs</span></div><div class='xr-var-dims'>(PCs_0, PCs_1)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838, 50), meta=np.ndarray></div><input id='attrs-536cb3cb-361b-44ef-aebf-b527591d0521' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-536cb3cb-361b-44ef-aebf-b527591d0521' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d8f107af-963c-4189-88f3-e0195acdab31' class='xr-var-data-in' type='checkbox'><label for='data-d8f107af-963c-4189-88f3-e0195acdab31' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " <td> 717.97 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " <td> (1838, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"80\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"30\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"30\" y1=\"0\" x2=\"30\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 30.80809411591093,0.0 30.80809411591093,120.0 0.0,120.0\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
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| " <text x=\"15.404047\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"50.808094\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,50.808094,60.000000)\">1838</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_pca</span></div><div class='xr-var-dims'>(X_pca_0, X_pca_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 50), meta=np.ndarray></div><input id='attrs-fb201d8f-f488-45b7-a623-dc5a415c80d3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb201d8f-f488-45b7-a623-dc5a415c80d3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d4e6ae44-0c78-44a0-9ea9-c61ad03b0ea0' class='xr-var-data-in' type='checkbox'><label for='data-d4e6ae44-0c78-44a0-9ea9-c61ad03b0ea0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"78\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"28\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
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| " <text x=\"14.364907\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
| " <text x=\"48.729813\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,48.729813,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>X_umap</span></div><div class='xr-var-dims'>(X_umap_0, X_umap_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 2), meta=np.ndarray></div><input id='attrs-cec1bc95-cfc2-44df-afcc-d0030acdf622' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cec1bc95-cfc2-44df-afcc-d0030acdf622' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76d025d3-ae90-4d9d-b39e-9aa24218f90f' class='xr-var-data-in' type='checkbox'><label for='data-76d025d3-ae90-4d9d-b39e-9aa24218f90f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " <td> (2638, 2) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"75\" height=\"170\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"25\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"120\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
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| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"25\" y1=\"0\" x2=\"25\" y2=\"120\" style=\"stroke-width:2\" />\n", | |
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| " <text x=\"45.412617\" y=\"60.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(-90,45.412617,60.000000)\">2638</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-adc97f1a-61c7-4f24-987e-2646820158cc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-adc97f1a-61c7-4f24-987e-2646820158cc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-472026c3-df00-4db0-a227-e34469aea556' class='xr-var-data-in' type='checkbox'><label for='data-472026c3-df00-4db0-a227-e34469aea556' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"170\" height=\"75\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
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| " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
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| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>dispersions_norm</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-5cb9ccab-b559-4e86-b54d-88e4025472ef' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5cb9ccab-b559-4e86-b54d-88e4025472ef' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a15cc324-00d8-4335-829f-4d5184c8de09' class='xr-var-data-in' type='checkbox'><label for='data-a15cc324-00d8-4335-829f-4d5184c8de09' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 7.18 kiB </td>\n", | |
| " <td> 7.18 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>gene_ids</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-6043bac1-ec71-4226-85f8-4a93f761fd81' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6043bac1-ec71-4226-85f8-4a93f761fd81' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5429557b-58bf-44ac-b31c-8d52b87d0af7' class='xr-var-data-in' type='checkbox'><label for='data-5429557b-58bf-44ac-b31c-8d52b87d0af7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>highly_variable</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-ce83da5d-0925-4ce3-8443-8bb244002112' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ce83da5d-0925-4ce3-8443-8bb244002112' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4e1b41e2-f310-446c-a7cd-bc5be9385267' class='xr-var-data-in' type='checkbox'><label for='data-4e1b41e2-f310-446c-a7cd-bc5be9385267' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 1.79 kiB </td>\n", | |
| " <td> 1.79 kiB </td>\n", | |
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| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> bool </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>leiden</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638,), meta=np.ndarray></div><input id='attrs-7dcb9795-73d5-414b-b35d-b412ae6e0c3a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7dcb9795-73d5-414b-b35d-b412ae6e0c3a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-614e4827-e7bf-421f-8efa-f7b6fa98708b' class='xr-var-data-in' type='checkbox'><label for='data-614e4827-e7bf-421f-8efa-f7b6fa98708b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <tr>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " <td> 20.61 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <td> (2638,) </td>\n", | |
| " <td> (2638,) </td>\n", | |
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| " <tr>\n", | |
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| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-c86b0547-8193-4d60-ac44-070998f0455d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c86b0547-8193-4d60-ac44-070998f0455d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5abdea74-de25-498e-be5d-76b65882a76f' class='xr-var-data-in' type='checkbox'><label for='data-5abdea74-de25-498e-be5d-76b65882a76f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <tr>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
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| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
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| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-560f0f60-c5f0-49fa-89d3-1e25ab3be70b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-560f0f60-c5f0-49fa-89d3-1e25ab3be70b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-79eb543c-35a0-4bc3-bb06-993534764816' class='xr-var-data-in' type='checkbox'><label for='data-79eb543c-35a0-4bc3-bb06-993534764816' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <td> (13714,) </td>\n", | |
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| " <tr>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-bf93400f-4219-467b-bf52-2b6b505730ad' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bf93400f-4219-467b-bf52-2b6b505730ad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1cf08dc2-930a-4dc4-9baf-96b698d30b70' class='xr-var-data-in' type='checkbox'><label for='data-1cf08dc2-930a-4dc4-9baf-96b698d30b70' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <td> (13714,) </td>\n", | |
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| " <td> float32 </td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-3b20c191-9b38-4c5e-b779-339d75bf3ce2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3b20c191-9b38-4c5e-b779-339d75bf3ce2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee1c9f67-1e39-483d-948d-92f597b6a0bb' class='xr-var-data-in' type='checkbox'><label for='data-ee1c9f67-1e39-483d-948d-92f597b6a0bb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
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| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-2bd18319-9848-4559-b2bb-ad3cf6514198' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2bd18319-9848-4559-b2bb-ad3cf6514198' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e6b82853-2fbc-4081-8be2-0ab1ff5a1c09' class='xr-var-data-in' type='checkbox'><label for='data-e6b82853-2fbc-4081-8be2-0ab1ff5a1c09' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
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| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-3bfd406a-b200-4f34-9fe8-7f2117e4036b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3bfd406a-b200-4f34-9fe8-7f2117e4036b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8288d6fb-6866-43f4-9022-44f049404fec' class='xr-var-data-in' type='checkbox'><label for='data-8288d6fb-6866-43f4-9022-44f049404fec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-56cbc019-3a06-42f2-ae2a-7193f39b1bc4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-56cbc019-3a06-42f2-ae2a-7193f39b1bc4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6c39c3e6-4286-4ba0-a5f2-85e3e2c4f00f' class='xr-var-data-in' type='checkbox'><label for='data-6c39c3e6-4286-4ba0-a5f2-85e3e2c4f00f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
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| " <th> Array </th>\n", | |
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| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>logfoldchanges_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-48ef1dc4-67f2-4a4c-96e7-cd60a719549b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-48ef1dc4-67f2-4a4c-96e7-cd60a719549b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b85b4a5b-976f-48f3-a36a-f609377f7581' class='xr-var-data-in' type='checkbox'><label for='data-b85b4a5b-976f-48f3-a36a-f609377f7581' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " <td> 53.57 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
| " <td> (13714,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-3690dc15-4124-4519-8551-0dcfe99612fa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3690dc15-4124-4519-8551-0dcfe99612fa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fb1b60c1-b77c-421b-8440-451acb4f64a3' class='xr-var-data-in' type='checkbox'><label for='data-fb1b60c1-b77c-421b-8440-451acb4f64a3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mean_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-9e692f73-c5b1-4e22-b326-ea261692e69b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9e692f73-c5b1-4e22-b326-ea261692e69b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b462a56e-de9f-41e7-a32b-b9eda92b025c' class='xr-var-data-in' type='checkbox'><label for='data-b462a56e-de9f-41e7-a32b-b9eda92b025c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 7.18 kiB </td>\n", | |
| " <td> 7.18 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>means</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-8d3bef7c-c0ab-4c45-8b78-23447e3d59ad' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8d3bef7c-c0ab-4c45-8b78-23447e3d59ad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c1987ba5-3631-4315-88f8-effb1a150466' class='xr-var-data-in' type='checkbox'><label for='data-c1987ba5-3631-4315-88f8-effb1a150466' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"170\" height=\"75\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>mt</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-827e1eae-4f15-430f-9c2e-ece5865edeec' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-827e1eae-4f15-430f-9c2e-ece5865edeec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08ae9022-278a-42c4-bdef-3aacca3a5ee0' class='xr-var-data-in' type='checkbox'><label for='data-08ae9022-278a-42c4-bdef-3aacca3a5ee0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 1.79 kiB </td>\n", | |
| " <td> 1.79 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> bool </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-fb9de2ab-0007-4b58-a8d1-fe6708d289c8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb9de2ab-0007-4b58-a8d1-fe6708d289c8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ca751774-086a-4ce8-88bc-161e83d29929' class='xr-var-data-in' type='checkbox'><label for='data-ca751774-086a-4ce8-88bc-161e83d29929' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> int64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"170\" height=\"75\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
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| " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
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| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_cells_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-7c31d102-d024-44e1-ba03-9f9e76699aca' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7c31d102-d024-44e1-ba03-9f9e76699aca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b60e8ff0-1589-4c56-92c0-d397aa0eddc1' class='xr-var-data-in' type='checkbox'><label for='data-b60e8ff0-1589-4c56-92c0-d397aa0eddc1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> int64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_genes</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638,), meta=np.ndarray></div><input id='attrs-0665cf44-b6e3-419d-8226-12f39cf0298e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0665cf44-b6e3-419d-8226-12f39cf0298e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4394ea97-f56b-4a3c-b2eb-43d0db169321' class='xr-var-data-in' type='checkbox'><label for='data-4394ea97-f56b-4a3c-b2eb-43d0db169321' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " <td> 20.61 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638,) </td>\n", | |
| " <td> (2638,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> int64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
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| " </td>\n", | |
| " <td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>n_genes_by_counts</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638,), meta=np.ndarray></div><input id='attrs-7925b09e-4537-4a1c-b4ad-e1104ee3c091' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7925b09e-4537-4a1c-b4ad-e1104ee3c091' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b3ead43f-5b5e-4447-bdc7-54eb3e97eff0' class='xr-var-data-in' type='checkbox'><label for='data-b3ead43f-5b5e-4447-bdc7-54eb3e97eff0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <tr>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 10.30 kiB </td>\n", | |
| " <td> 10.30 kiB </td>\n", | |
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| " <tr>\n", | |
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| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> int32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_B</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-4058a7fc-0c7f-43b2-8b99-df3e9831b969' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4058a7fc-0c7f-43b2-8b99-df3e9831b969' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-32e8e5ff-49ca-4439-9ff0-5f2aaf6cc274' class='xr-var-data-in' type='checkbox'><label for='data-32e8e5ff-49ca-4439-9ff0-5f2aaf6cc274' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD14 Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-e201c11b-0df5-4d52-853a-91a03ddf7e45' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e201c11b-0df5-4d52-853a-91a03ddf7e45' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7ff5ab7e-e964-4779-865e-4ed5f506ac13' class='xr-var-data-in' type='checkbox'><label for='data-7ff5ab7e-e964-4779-865e-4ed5f506ac13' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD4 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-31e80949-f286-4f99-b1db-d8b5ba8ef45c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-31e80949-f286-4f99-b1db-d8b5ba8ef45c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8298231-0b3e-4550-8685-5f966d9592b9' class='xr-var-data-in' type='checkbox'><label for='data-e8298231-0b3e-4550-8685-5f966d9592b9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <td>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
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| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_CD8 T</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-2e1f2549-b348-4524-a9ca-dda2767ea183' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2e1f2549-b348-4524-a9ca-dda2767ea183' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d880bdc5-4168-49e1-a70c-ea87efa4feb6' class='xr-var-data-in' type='checkbox'><label for='data-d880bdc5-4168-49e1-a70c-ea87efa4feb6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
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| " <td> (13714,) </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Dendritic</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-0de0b3e9-4748-4501-8459-864ae1aa53bf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0de0b3e9-4748-4501-8459-864ae1aa53bf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9633fa96-e92d-4999-a4ac-b84d10a6c390' class='xr-var-data-in' type='checkbox'><label for='data-9633fa96-e92d-4999-a4ac-b84d10a6c390' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_FCGR3A Monocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-056cedae-e640-438a-b098-5d9025fc8380' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-056cedae-e640-438a-b098-5d9025fc8380' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-14c5d8b9-ab03-4fa6-bf1b-29f07c4dec1b' class='xr-var-data-in' type='checkbox'><label for='data-14c5d8b9-ab03-4fa6-bf1b-29f07c4dec1b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
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| " </table>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_Megakaryocytes</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-29160860-ac9a-4200-9cbc-b7e2ea15ff4b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-29160860-ac9a-4200-9cbc-b7e2ea15ff4b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-afc76fff-d6ec-4180-a78b-dd7cdba1a667' class='xr-var-data-in' type='checkbox'><label for='data-afc76fff-d6ec-4180-a78b-dd7cdba1a667' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (13714,) </td>\n", | |
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| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
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| " </table>\n", | |
| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>names_NK</span></div><div class='xr-var-dims'>(rank_genes_groups)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(13714,), meta=np.ndarray></div><input id='attrs-341ecd14-4ff6-4480-9914-a635a1fae2d6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-341ecd14-4ff6-4480-9914-a635a1fae2d6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3080c626-2cb7-4035-b7a6-36749b27c3bc' class='xr-var-data-in' type='checkbox'><label for='data-3080c626-2cb7-4035-b7a6-36749b27c3bc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 107.14 kiB </td>\n", | |
| " <td> 107.14 kiB </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
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| " </table>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_counts_mt</span></div><div class='xr-var-dims'>(obs)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638,), meta=np.ndarray></div><input id='attrs-bad29699-b773-4572-b039-f4dc6a625210' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bad29699-b773-4572-b039-f4dc6a625210' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e940b88a-887d-4688-bbb0-e81954e56741' class='xr-var-data-in' type='checkbox'><label for='data-e940b88a-887d-4688-bbb0-e81954e56741' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 10.30 kiB </td>\n", | |
| " <td> 10.30 kiB </td>\n", | |
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| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638,) </td>\n", | |
| " <td> (2638,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
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| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
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| " </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>pct_dropout_by_counts</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-2025cf18-10c3-433e-bf32-1a6f8531130f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2025cf18-10c3-433e-bf32-1a6f8531130f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-17168371-6bb9-4181-a690-7a75befe7a54' class='xr-var-data-in' type='checkbox'><label for='data-17168371-6bb9-4181-a690-7a75befe7a54' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
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| " \n", | |
| " <tr>\n", | |
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| " <td> (1838,) </td>\n", | |
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| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
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| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>std</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-d919b7af-a8a1-486d-90e7-6cb4bc002b4b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d919b7af-a8a1-486d-90e7-6cb4bc002b4b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fe6f3b2b-7d32-4732-a42c-defac1bc0ca6' class='xr-var-data-in' type='checkbox'><label for='data-fe6f3b2b-7d32-4732-a42c-defac1bc0ca6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
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| " <tr>\n", | |
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| " <tbody>\n", | |
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| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
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| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
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| "<xarray.Dataset>\n", | |
| "Dimensions: (PCs_0: 1838, PCs_1: 50, X_pca_0: 2638,\n", | |
| " X_pca_1: 50, X_umap_0: 2638, X_umap_1: 2,\n", | |
| " vars: 1838, genes_groups: 8, obs: 2638,\n", | |
| " rank_genes_groups: 13714)\n", | |
| "Coordinates:\n", | |
| " * PCs_0 (PCs_0) int64 0 1 2 3 ... 1835 1836 1837\n", | |
| " * PCs_1 (PCs_1) int64 0 1 2 3 4 ... 45 46 47 48 49\n", | |
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| " * genes_groups (genes_groups) <U16 'CD4 T' ... 'Megakar...\n", | |
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| "Data variables: (12/37)\n", | |
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| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray>\n", | |
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| " gene_ids (vars) object dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " ... ...\n", | |
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| " total_counts_mt (obs) float32 dask.array<chunksize=(2638,), meta=np.ndarray>" | |
| ] | |
| }, | |
| "execution_count": 26, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata_ds_zarr" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Selecting Data\n", | |
| "\n", | |
| "You can access the xarray data variables as an dictionary key." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 27, | |
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| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (X_pca_0: 2638, X_pca_1: 50)\n", | |
| "Coordinates:\n", | |
| " * X_pca_0 (X_pca_0) int64 0 1 2 3 4 5 6 ... 2632 2633 2634 2635 2636 2637\n", | |
| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 5 6 7 8 9 ... 41 42 43 44 45 46 47 48 49\n", | |
| "Data variables:\n", | |
| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray></pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-48e13321-741b-4d51-835b-06c44c26dc4f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-48e13321-741b-4d51-835b-06c44c26dc4f' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>X_pca_0</span>: 2638</li><li><span class='xr-has-index'>X_pca_1</span>: 50</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-33082cc2-fb1e-4392-900e-4eaf5475ebdc' class='xr-section-summary-in' type='checkbox' checked><label for='section-33082cc2-fb1e-4392-900e-4eaf5475ebdc' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_0</span></div><div class='xr-var-dims'>(X_pca_0)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 ... 2634 2635 2636 2637</div><input id='attrs-857d2c2f-0681-45bf-9f7a-43ed83958c96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-857d2c2f-0681-45bf-9f7a-43ed83958c96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c9c1458-bbb4-48da-a8ae-b3b98b7f285b' class='xr-var-data-in' type='checkbox'><label for='data-5c9c1458-bbb4-48da-a8ae-b3b98b7f285b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 2635, 2636, 2637])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>X_pca_1</span></div><div class='xr-var-dims'>(X_pca_1)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 44 45 46 47 48 49</div><input id='attrs-913f4c72-c3d9-4408-830e-b4b77b376586' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-913f4c72-c3d9-4408-830e-b4b77b376586' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0c85ec7c-8633-4d85-8cc3-b9f0c3a4ea6b' class='xr-var-data-in' type='checkbox'><label for='data-0c85ec7c-8633-4d85-8cc3-b9f0c3a4ea6b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n", | |
| " 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,\n", | |
| " 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-182f84b7-c51b-4791-9803-fcbdb51e0e02' class='xr-section-summary-in' type='checkbox' checked><label for='section-182f84b7-c51b-4791-9803-fcbdb51e0e02' class='xr-section-summary' >Data variables: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>X_pca</span></div><div class='xr-var-dims'>(X_pca_0, X_pca_1)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(2638, 50), meta=np.ndarray></div><input id='attrs-963eecee-eabe-42f3-ad36-93f294148dd2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-963eecee-eabe-42f3-ad36-93f294148dd2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cfa96142-1bb0-4390-b5bb-dc845fac620e' class='xr-var-data-in' type='checkbox'><label for='data-cfa96142-1bb0-4390-b5bb-dc845fac620e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " <td> 515.23 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " <td> (2638, 50) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float32 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
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| " <text x=\"14.364907\" y=\"140.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n", | |
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| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-e6fb01f9-339e-4093-8617-26291edf0887' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e6fb01f9-339e-4093-8617-26291edf0887' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
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| "Dimensions: (X_pca_0: 2638, X_pca_1: 50)\n", | |
| "Coordinates:\n", | |
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| " * X_pca_1 (X_pca_1) int64 0 1 2 3 4 5 6 7 8 9 ... 41 42 43 44 45 46 47 48 49\n", | |
| "Data variables:\n", | |
| " X_pca (X_pca_0, X_pca_1) float32 dask.array<chunksize=(2638, 50), meta=np.ndarray>" | |
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| ".xr-sections {\n", | |
| " padding-left: 0 !important;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 150px auto auto 1fr 20px 20px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input + label {\n", | |
| " color: var(--xr-disabled-color);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input:enabled + label {\n", | |
| " cursor: pointer;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-item input:enabled + label:hover {\n", | |
| " color: var(--xr-font-color0);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary {\n", | |
| " grid-column: 1;\n", | |
| " color: var(--xr-font-color2);\n", | |
| " font-weight: 500;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary > span {\n", | |
| " display: inline-block;\n", | |
| " padding-left: 0.5em;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:disabled + label {\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in + label:before {\n", | |
| " display: inline-block;\n", | |
| " content: '►';\n", | |
| " font-size: 11px;\n", | |
| " width: 15px;\n", | |
| " text-align: center;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:disabled + label:before {\n", | |
| " color: var(--xr-disabled-color);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:checked + label:before {\n", | |
| " content: '▼';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:checked + label > span {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary,\n", | |
| ".xr-section-inline-details {\n", | |
| " padding-top: 4px;\n", | |
| " padding-bottom: 4px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-inline-details {\n", | |
| " grid-column: 2 / -1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-details {\n", | |
| " display: none;\n", | |
| " grid-column: 1 / -1;\n", | |
| " margin-bottom: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-section-summary-in:checked ~ .xr-section-details {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-wrap {\n", | |
| " grid-column: 1 / -1;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 20px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-wrap > label {\n", | |
| " grid-column: 1;\n", | |
| " vertical-align: top;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-preview {\n", | |
| " color: var(--xr-font-color3);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-preview,\n", | |
| ".xr-array-data {\n", | |
| " padding: 0 5px !important;\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-data,\n", | |
| ".xr-array-in:checked ~ .xr-array-preview {\n", | |
| " display: none;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-array-in:checked ~ .xr-array-data,\n", | |
| ".xr-array-preview {\n", | |
| " display: inline-block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list {\n", | |
| " display: inline-block !important;\n", | |
| " list-style: none;\n", | |
| " padding: 0 !important;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li {\n", | |
| " display: inline-block;\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:before {\n", | |
| " content: '(';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list:after {\n", | |
| " content: ')';\n", | |
| "}\n", | |
| "\n", | |
| ".xr-dim-list li:not(:last-child):after {\n", | |
| " content: ',';\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-has-index {\n", | |
| " font-weight: bold;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list,\n", | |
| ".xr-var-item {\n", | |
| " display: contents;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > div,\n", | |
| ".xr-var-item label,\n", | |
| ".xr-var-item > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-even);\n", | |
| " margin-bottom: 0;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-item > .xr-var-name:hover span {\n", | |
| " padding-right: 5px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-list > li:nth-child(odd) > div,\n", | |
| ".xr-var-list > li:nth-child(odd) > label,\n", | |
| ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n", | |
| " background-color: var(--xr-background-color-row-odd);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name {\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dims {\n", | |
| " grid-column: 2;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-dtype {\n", | |
| " grid-column: 3;\n", | |
| " text-align: right;\n", | |
| " color: var(--xr-font-color2);\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-preview {\n", | |
| " grid-column: 4;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name,\n", | |
| ".xr-var-dims,\n", | |
| ".xr-var-dtype,\n", | |
| ".xr-preview,\n", | |
| ".xr-attrs dt {\n", | |
| " white-space: nowrap;\n", | |
| " overflow: hidden;\n", | |
| " text-overflow: ellipsis;\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name:hover,\n", | |
| ".xr-var-dims:hover,\n", | |
| ".xr-var-dtype:hover,\n", | |
| ".xr-attrs dt:hover {\n", | |
| " overflow: visible;\n", | |
| " width: auto;\n", | |
| " z-index: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " display: none;\n", | |
| " background-color: var(--xr-background-color) !important;\n", | |
| " padding-bottom: 5px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", | |
| ".xr-var-data-in:checked ~ .xr-var-data {\n", | |
| " display: block;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-data > table {\n", | |
| " float: right;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-var-name span,\n", | |
| ".xr-var-data,\n", | |
| ".xr-attrs {\n", | |
| " padding-left: 25px !important;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs,\n", | |
| ".xr-var-attrs,\n", | |
| ".xr-var-data {\n", | |
| " grid-column: 1 / -1;\n", | |
| "}\n", | |
| "\n", | |
| "dl.xr-attrs {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " display: grid;\n", | |
| " grid-template-columns: 125px auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt,\n", | |
| ".xr-attrs dd {\n", | |
| " padding: 0;\n", | |
| " margin: 0;\n", | |
| " float: left;\n", | |
| " padding-right: 10px;\n", | |
| " width: auto;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt {\n", | |
| " font-weight: normal;\n", | |
| " grid-column: 1;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dt:hover span {\n", | |
| " display: inline-block;\n", | |
| " background: var(--xr-background-color);\n", | |
| " padding-right: 10px;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-attrs dd {\n", | |
| " grid-column: 2;\n", | |
| " white-space: pre-wrap;\n", | |
| " word-break: break-all;\n", | |
| "}\n", | |
| "\n", | |
| ".xr-icon-database,\n", | |
| ".xr-icon-file-text2 {\n", | |
| " display: inline-block;\n", | |
| " vertical-align: middle;\n", | |
| " width: 1em;\n", | |
| " height: 1.5em !important;\n", | |
| " stroke-width: 0;\n", | |
| " stroke: currentColor;\n", | |
| " fill: currentColor;\n", | |
| "}\n", | |
| "</style><pre class='xr-text-repr-fallback'><xarray.Dataset>\n", | |
| "Dimensions: (vars: 1838)\n", | |
| "Coordinates:\n", | |
| " * vars (vars) object 'TNFRSF4' 'CPSF3L' 'ATAD3C' ... 'S100B' 'PRMT2'\n", | |
| "Data variables:\n", | |
| " mean (vars) float64 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " gene_ids (vars) object dask.array<chunksize=(1838,), meta=np.ndarray></pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-f92bd256-f109-46f4-9112-cd5e52776283' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f92bd256-f109-46f4-9112-cd5e52776283' class='xr-section-summary' title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>vars</span>: 1838</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-595ab1ec-96b2-4b14-a5d6-b7e9322fd1d5' class='xr-section-summary-in' type='checkbox' checked><label for='section-595ab1ec-96b2-4b14-a5d6-b7e9322fd1d5' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>vars</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>'TNFRSF4' 'CPSF3L' ... 'PRMT2'</div><input id='attrs-a0bbcbf8-3422-49ab-8bfb-b0d744badc0d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a0bbcbf8-3422-49ab-8bfb-b0d744badc0d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8a90b2f6-a8ec-4029-8c5a-350ac98b94c0' class='xr-var-data-in' type='checkbox'><label for='data-8a90b2f6-a8ec-4029-8c5a-350ac98b94c0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array(['TNFRSF4', 'CPSF3L', 'ATAD3C', ..., 'SLC19A1', 'S100B', 'PRMT2'],\n", | |
| " dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f51f69ec-e8e5-4cb4-b5ae-f7a5c82c7194' class='xr-section-summary-in' type='checkbox' checked><label for='section-f51f69ec-e8e5-4cb4-b5ae-f7a5c82c7194' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>mean</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-0394e23d-81a4-44d2-afa8-76e73316544e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0394e23d-81a4-44d2-afa8-76e73316544e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-518d9cfc-f15c-4603-a56c-9aec0901ba8e' class='xr-var-data-in' type='checkbox'><label for='data-518d9cfc-f15c-4603-a56c-9aec0901ba8e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> float64 </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"170\" height=\"75\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"25\" x2=\"120\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 120.0,0.0 120.0,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"60.000000\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1838</text>\n", | |
| " <text x=\"140.000000\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,140.000000,12.706308)\">1</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>gene_ids</span></div><div class='xr-var-dims'>(vars)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array<chunksize=(1838,), meta=np.ndarray></div><input id='attrs-e6c78842-3202-47b5-b119-e29929aeb49d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e6c78842-3202-47b5-b119-e29929aeb49d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-83f6cc90-be97-4438-a5db-56a00e2e2ae7' class='xr-var-data-in' type='checkbox'><label for='data-83f6cc90-be97-4438-a5db-56a00e2e2ae7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>\n", | |
| " <tr>\n", | |
| " <td>\n", | |
| " <table>\n", | |
| " <thead>\n", | |
| " <tr>\n", | |
| " <td> </td>\n", | |
| " <th> Array </th>\n", | |
| " <th> Chunk </th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Bytes </th>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " <td> 14.36 kiB </td>\n", | |
| " </tr>\n", | |
| " \n", | |
| " <tr>\n", | |
| " <th> Shape </th>\n", | |
| " <td> (1838,) </td>\n", | |
| " <td> (1838,) </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Count </th>\n", | |
| " <td> 2 Tasks </td>\n", | |
| " <td> 1 Chunks </td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th> Type </th>\n", | |
| " <td> object </td>\n", | |
| " <td> numpy.ndarray </td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| " </table>\n", | |
| " </td>\n", | |
| " <td>\n", | |
| " <svg width=\"170\" height=\"75\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n", | |
| "\n", | |
| " <!-- Horizontal lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"0\" y1=\"25\" x2=\"120\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Vertical lines -->\n", | |
| " <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| " <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"25\" style=\"stroke-width:2\" />\n", | |
| "\n", | |
| " <!-- Colored Rectangle -->\n", | |
| " <polygon points=\"0.0,0.0 120.0,0.0 120.0,25.412616514582485 0.0,25.412616514582485\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n", | |
| "\n", | |
| " <!-- Text -->\n", | |
| " <text x=\"60.000000\" y=\"45.412617\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >1838</text>\n", | |
| " <text x=\"140.000000\" y=\"12.706308\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,140.000000,12.706308)\">1</text>\n", | |
| "</svg>\n", | |
| " </td>\n", | |
| " </tr>\n", | |
| "</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-0d746169-7b37-4b77-b6ca-32f065033b5c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0d746169-7b37-4b77-b6ca-32f065033b5c' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>" | |
| ], | |
| "text/plain": [ | |
| "<xarray.Dataset>\n", | |
| "Dimensions: (vars: 1838)\n", | |
| "Coordinates:\n", | |
| " * vars (vars) object 'TNFRSF4' 'CPSF3L' 'ATAD3C' ... 'S100B' 'PRMT2'\n", | |
| "Data variables:\n", | |
| " mean (vars) float64 dask.array<chunksize=(1838,), meta=np.ndarray>\n", | |
| " gene_ids (vars) object dask.array<chunksize=(1838,), meta=np.ndarray>" | |
| ] | |
| }, | |
| "execution_count": 28, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "adata_ds_zarr[['mean', 'gene_ids']]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "pycharm": { | |
| "name": "#%% md\n" | |
| } | |
| }, | |
| "source": [ | |
| "## Plotting\n", | |
| "\n", | |
| "Seaborn and matplotlib each play well with dataframes.\n", | |
| "\n", | |
| "WIP" | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "anaconda-cloud": {}, | |
| "kernelspec": { | |
| "display_name": "Python 3 (ipykernel)", | |
| "language": "python", | |
| "name": "python3" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.10.4" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 4 | |
| } |
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