Gregor Sturm grst
grst
/ airr-json.ipynb
Created
June 13, 2023 17:55
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grst
/ squidpy_get_bbox.py
Created
August 2, 2023 13:31
Get bounding box for squidpy spatial plot to be equivalent to the scanpy.pl.spatial
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| def get_bbox(adata, library_id, *, library_key="sample", img_key="hires", margin=50): | |
| adata = adata[adata.obs[library_key] == library_id, :] | |
| coords = adata.obsm["spatial"] | |
| scale_factor = adata.uns["spatial"][library_id]["scalefactors"][f"tissue_{img_key}_scalef"] | |
| return tuple( | |
| np.array( | |
| [ | |
| np.min(coords[:, 0]) - margin, | |
| np.min(coords[:, 1]) - margin, | |
| np.max(coords[:, 0]) + margin, |
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| from functools import partial | |
| import math | |
| from typing import Literal | |
| from datashader.mpl_ext import dsshow, alpha_colormap | |
| import datashader as ds | |
| from joblib import parallel_backend | |
| from mpl_toolkits.axes_grid1 import ImageGrid | |
| import matplotlib.pyplot as plt | |
| import pandas as pd | |
| import scanpy as sc |
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