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ElDeveloper/16S-and-lcms-mangling.ipynb

Created April 27, 2017 00:58
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16S-and-lcms-mangling.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import pandas as pd, numpy as np"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"def load_mf(fn, index='#SampleID'):\n",
" _df = pd.read_csv(fn, sep='\\t', dtype=str,\n",
" keep_default_na=False, na_values=[])\n",
" _df.set_index(index, inplace=True)\n",
" return _df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Theodore sent me a link to this zip archive."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"!unzip 3D_humanskin_share.zip"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ls"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Create some additional metadata categories based on the bodypart category."
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def to_metadata(fn):\n",
" _df = pd.read_excel(fn).astype(str)\n",
"\n",
" _df['#SampleID'] = _df['plate'] + '_' + _df['row'] + '_' + _df['column']\n",
" _df.set_index('#SampleID', inplace=True)\n",
"\n",
" _df['top_or_bottom'] = _df.bodypart.replace({'LEGBACK': 'Bottom', 'FACE': 'Top', 'HEADTOP': 'Top',\n",
" 'HEADBACK': 'Top', 'EAR': 'Top', 'FACE': 'Top',\n",
" 'LIPS': 'Top', 'SHOULDERBACK': 'Top', 'SHOULDERFRONT': 'Top',\n",
" 'PECTORAL': 'Top', 'HANDFRONT': 'Top', 'HANDBACK': 'Top',\n",
" 'ARM': 'Top', 'SIDE': 'Top', 'LEGFRONT': 'Bottom',\n",
" 'FOOTTOP': 'Bottom', 'BACK': 'Top', 'FRONT': 'Top',\n",
" 'LEGINSIDE': 'Bottom', 'LEGOUTSIDE': 'Bottom', 'GROIN': 'Bottom',\n",
" 'LEGBACK': 'Bottom', 'FOOTBOTTOM': 'Bottom'})\n",
"\n",
" _df['plane'] = _df.bodypart.replace({'LEGBACK': 'Posterior', 'FACE': 'Anterior',\n",
" 'HEADTOP': 'Anterior', 'HEADBACK': 'Posterior', 'EAR': 'Lateral',\n",
" 'FACE': 'Anterior', 'LIPS': 'Anterior', 'SHOULDERBACK': 'Posterior',\n",
" 'SHOULDERFRONT': 'Anterior', 'PECTORAL': 'Anterior', 'HANDFRONT': 'Anterior',\n",
" 'HANDBACK': 'Posterior', 'ARM': 'Lateral', 'SIDE': 'Lateral',\n",
" 'LEGFRONT': 'Anterior', 'FOOTTOP': 'Anterior', 'BACK': 'Posterior',\n",
" 'FRONT': 'Anterior', 'LEGINSIDE': 'Lateral', 'LEGOUTSIDE': 'Lateral',\n",
" 'GROIN': 'Anterior', 'LEGBACK': 'Posterior', 'FOOTBOTTOM': 'Plantar'})\n",
"\n",
" _df['clothed'] = _df.bodypart.replace({'LEGBACK': 'Yes', 'FACE': 'No', 'HEADTOP': 'No',\n",
" 'HEADBACK': 'No', 'EAR': 'No', 'FACE': 'No',\n",
" 'LIPS': 'No', 'SHOULDERBACK': 'Yes', 'SHOULDERFRONT': 'Yes',\n",
" 'PECTORAL': 'Yes', 'HANDFRONT': 'No', 'HANDBACK': 'No',\n",
" 'ARM': 'Yes', 'SIDE': 'Yes', 'LEGFRONT': 'Yes',\n",
" 'FOOTTOP': 'Yes', 'BACK': 'Yes', 'FRONT': 'Yes',\n",
" 'LEGINSIDE': 'Yes', 'LEGOUTSIDE': 'Yes', 'GROIN': 'Yes',\n",
" 'LEGBACK': 'Yes', 'FOOTBOTTOM': 'Yes'})\n",
" return _df"
]
},
{
"cell_type": "code",
"execution_count": 65,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"to_metadata('annotation_man.xlsx').to_csv('annotation-man.tsv', sep='\\t')\n",
"to_metadata('annotation_woman.xlsx').to_csv('annotation-woman.tsv', sep='\\t')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ls *.csv"
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import scipy\n",
"\n",
"from skbio import DistanceMatrix\n",
"from skbio.diversity import beta_diversity\n",
"from skbio.stats.ordination import pcoa"
]
},
{
"cell_type": "code",
"execution_count": 56,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"table = pd.read_csv('m_LCMS.csv').set_index('plate_row_column')\n",
"table.drop(['x', 'y', 'z', 'radii'], axis=1, inplace=True)\n",
"table.fillna(0, inplace=True)\n",
"\n",
"non_empty_samples = (table.T.sum() > 0)\n",
"table = table.loc[non_empty_samples.values].copy()\n",
"\n",
"non_empty_otus = (table.sum() > 0)\n",
"table = table[table.sum()[non_empty_otus].index].copy()"
]
},
{
"cell_type": "code",
"execution_count": 59,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<script type=\"text/javascript\">\n",
"\n",
"if ($(\"#emperor-css\").length == 0){{\n",
" $(\"head\").append([\n",
"\n",
" '<link id=\"emperor-css\" rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/css/emperor.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/css/jquery-ui.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/css/slick.grid.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/css/spectrum.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/css/chosen.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/css/jquery.contextMenu.min.css\">'\n",
" ]);\n",
"}}\n",
"</script>\n",
"\n",
"<div id='emperor-notebook-0x8db74d51' style=\"position: relative; width:100%; height:500px;\">\n",
" <div class='loading' style=\"position: absolute;top: 50%;left: 50%;margin-left: -229px; margin-top: -59px; z-index: 10000;height:118px;width:458px;padding:0px\"><img src='https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/img/emperor.png' alt='Emperor resources missing. Expected them to be found in https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files'></div>\n",
"</div>\n",
"</div>\n",
"\n",
"<script type=\"text/javascript\">\n",
"requirejs.config({\n",
"// the left side is the module name, and the right side is the path\n",
"// relative to the baseUrl attribute, do NOT include the .js extension\n",
"'paths': {\n",
" /* jQuery */\n",
" 'jquery': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/jquery-2.1.4.min',\n",
" 'jqueryui': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/jquery-ui.min',\n",
" 'jquery_drag': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/jquery.event.drag-2.2.min',\n",
"\n",
" /* jQuery plugins */\n",
" 'chosen': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/chosen.jquery.min',\n",
" 'spectrum': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/spectrum.min',\n",
" 'position': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/jquery.ui.position.min',\n",
" 'contextmenu': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/jquery.contextMenu.min',\n",
"\n",
" /* other libraries */\n",
" 'underscore': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/underscore-min',\n",
" 'chroma': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/chroma.min',\n",
" 'filesaver': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/FileSaver.min',\n",
" 'blob': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/Blob',\n",
" 'canvastoblob': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/canvas-toBlob',\n",
" 'd3': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/d3.min',\n",
"\n",
" /* THREE.js and plugins */\n",
" 'three': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/three.min',\n",
" 'orbitcontrols': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/three.js-plugins/OrbitControls',\n",
" 'projector': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/three.js-plugins/Projector',\n",
" 'svgrenderer': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/three.js-plugins/SVGRenderer',\n",
" 'canvasrenderer': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/three.js-plugins/CanvasRenderer',\n",
"\n",
" /* SlickGrid */\n",
" 'slickcore': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/slick.core.min',\n",
" 'slickgrid': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/slick.grid.min',\n",
" 'slickformatters': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/slick.editors.min',\n",
" 'slickeditors': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/vendor/js/slick.formatters.min',\n",
"\n",
" /* Emperor's objects */\n",
" 'util': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/util',\n",
" 'model': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/model',\n",
" 'view': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/view',\n",
" 'controller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/controller',\n",
" 'draw': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/draw',\n",
" 'scene3d': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/sceneplotview3d',\n",
" 'abcviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/abc-view-controller',\n",
" 'viewcontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/view-controller',\n",
" 'colorviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/color-view-controller',\n",
" 'visibilitycontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/visibility-controller',\n",
" 'scaleviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/scale-view-controller',\n",
" 'shapecontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/shape-controller',\n",
" 'axescontroller': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/axes-controller',\n",
" 'shape-editor': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/shape-editor',\n",
" 'color-editor': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/color-editor',\n",
" 'scale-editor': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/scale-editor',\n",
" 'shapes': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/js/shapes'\n",
"},\n",
"/*\n",
" Libraries that are not AMD compatible need shim to declare their\n",
" dependencies.\n",
" */\n",
"'shim': {\n",
" 'jquery_drag': {\n",
" 'deps': ['jquery', 'jqueryui']\n",
" },\n",
" 'chosen': {\n",
" 'deps': ['jquery'],\n",
" 'exports': 'jQuery.fn.chosen'\n",
" },\n",
" 'contextmenu' : {\n",
" 'deps': ['jquery', 'jqueryui', 'position']\n",
" },\n",
" 'filesaver' : {\n",
" 'deps': ['blob']\n",
" },\n",
" 'canvastoblob' : {\n",
" 'deps': ['blob']\n",
" },\n",
" 'slickcore': ['jqueryui'],\n",
" 'slickgrid': ['slickcore', 'jquery_drag', 'slickformatters', 'slickeditors']\n",
"}\n",
"});\n",
"\n",
"requirejs(\n",
"[\"jquery\", \"model\", \"controller\"],\n",
"function($, model, EmperorController) {\n",
" var DecompositionModel = model.DecompositionModel;\n",
"\n",
" var div = $('#emperor-notebook-0x8db74d51');\n",
"\n",
" var data = {\n",
" // coordinates information\n",
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" 'axes_names': [\"PC1\", \"PC2\", \"PC3\", \"PC4\", \"PC5\"],\n",
" 'percents_explained': [0.3663158793161946, 0.34823768703713187, 0.30417777773227433, 0.29917572550856436, 0.2897796538867227],\n",
"\n",
" // sample information\n",
" 'metadata_headers': [\"SampleID\", \"plate\", \"row\", \"column\", \"x\", \"y\", \"z\", \"bodypart\", \"radius\", \"x-offset\", \"y-offset\", \"z-offset\", \"top_or_bottom\", \"plane\", \"clothed\"],\n",
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\"Posterior\", \"Yes\"], [\"5_D_4\", \"5\", \"D\", \"4\", \"6.283903\", \"3.639048\", \"28.066149\", \"LEGBACK\", \"0.9\", \"0.0\", \"1.0\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_5\", \"5\", \"D\", \"5\", \"3.732384\", \"2.704\", \"26.904388\", \"LEGBACK\", \"0.9\", \"0.0\", \"1.0\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_6\", \"5\", \"D\", \"6\", \"5.193865\", \"3.181437\", \"25.026379\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_7\", \"5\", \"D\", \"7\", \"7.156055\", \"3.189316\", \"23.412777\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_8\", \"5\", \"D\", \"8\", \"4.940736\", \"2.571558\", \"22.553482\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_9\", \"5\", \"D\", \"9\", \"8.031176\", \"3.602306\", \"21.448936\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_10\", \"5\", \"D\", \"10\", \"5.846432\", \"3.285377\", \"20.437107\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_11\", \"5\", \"D\", \"11\", \"6.861727\", \"4.030803\", \"20.122019\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_D_12\", \"5\", \"D\", \"12\", \"8.494477\", \"4.415937\", \"19.536215\", \"LEGBACK\", \"0.8\", \"0.0\", \"0.9\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_1\", \"5\", \"E\", \"1\", \"5.861833\", \"3.677852\", \"19.028896\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_2\", \"5\", \"E\", \"2\", \"8.890194\", \"4.894144\", \"17.952274\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_3\", \"5\", \"E\", \"3\", \"7.192254\", \"4.727104\", \"18.392258\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_4\", \"5\", \"E\", \"4\", \"5.864395\", \"4.057693\", \"17.638664\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_5\", \"5\", \"E\", \"5\", \"7.327301\", \"5.010002\", \"17.253624\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_6\", \"5\", \"E\", \"6\", \"6.03677\", \"4.381237\", \"16.075136\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_7\", \"5\", \"E\", \"7\", \"9.241365\", \"5.198591\", \"16.001072\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_8\", \"5\", \"E\", \"8\", \"7.673422\", \"5.12976\", \"15.153869\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_9\", \"5\", \"E\", \"9\", \"9.215673\", \"5.212979\", \"14.289587\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_10\", \"5\", \"E\", \"10\", \"6.574753\", \"4.637589\", \"13.905399\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_11\", \"5\", \"E\", \"11\", \"8.310642\", \"5.173312\", \"13.454697\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_E_12\", \"5\", \"E\", \"12\", \"7.331748\", \"4.117722\", \"11.774769\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_1\", \"5\", \"F\", \"1\", \"9.736262\", \"4.71245\", \"12.23266\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_2\", \"5\", \"F\", \"2\", \"8.855\", \"5.060016\", \"10.650051\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_3\", \"5\", \"F\", \"3\", \"9.471601\", \"4.924827\", \"9.556675\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_4\", \"5\", \"F\", \"4\", \"8.691459\", \"4.81506\", \"8.541282\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_5\", \"5\", \"F\", \"5\", \"9.565533\", \"5.082736\", \"6.601761\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_6\", \"5\", \"F\", \"6\", \"9.29567\", \"4.102436\", \"3.746766\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_7\", \"5\", \"F\", \"7\", \"10.395904\", \"5.392444\", \"3.851792\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_8\", \"5\", \"F\", \"8\", \"9.167229\", \"6.184935\", \"2.206426\", \"LEGBACK\", \"0.7\", \"0.0\", \"0.75\", \"0.0\", \"Bottom\", \"Posterior\", \"Yes\"], [\"5_F_9\", \"5\", \"F\", \"9\", \"15.104148\", \"-3.800174\", \"0.127836\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_F_10\", \"5\", \"F\", \"10\", \"14.48003\", \"-3.477969\", \"-0.064672\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_F_11\", \"5\", \"F\", \"11\", \"13.675809\", \"-2.656492\", \"0.295415\", \"FOOTBOTTOM\", \"0.5\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_F_12\", \"5\", \"F\", \"12\", \"14.860248\", \"-2.201896\", \"0.34061\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_1\", \"5\", \"G\", \"1\", \"15.687577\", \"-3.028368\", \"-0.034806\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_2\", \"5\", \"G\", \"2\", \"15.827385\", \"-2.171436\", \"-0.091608\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_3\", \"5\", \"G\", \"3\", \"15.209572\", \"-1.41568\", \"0.299814\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_4\", \"5\", \"G\", \"4\", \"15.883177\", \"-1.308658\", \"-0.059144\", \"FOOTBOTTOM\", \"0.35\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_5\", \"5\", \"G\", \"5\", \"15.350082\", \"-0.55356\", \"0.279721\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_6\", \"5\", \"G\", \"6\", \"15.933833\", \"-0.298508\", \"-0.009217\", \"FOOTBOTTOM\", \"0.35\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_7\", \"5\", \"G\", \"7\", \"15.37978\", \"0.420455\", \"0.273385\", \"FOOTBOTTOM\", \"0.4\", \"0.0\", \"0.0\", \"-0.5\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_8\", \"5\", \"G\", \"8\", \"14.491364\", \"-1.314035\", \"0.041961\", \"FOOTBOTTOM\", \"0.5\", \"0.0\", \"0.0\", \"-0.6\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_9\", \"5\", \"G\", \"9\", \"13.043906\", \"-1.639182\", \"0.129708\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_10\", \"5\", \"G\", \"10\", \"13.696513\", \"-0.162133\", \"0.131764\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_11\", \"5\", \"G\", \"11\", \"12.370431\", \"-0.360748\", \"0.217684\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_G_12\", \"5\", \"G\", \"12\", \"13.839687\", \"1.142804\", \"0.166272\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_1\", \"5\", \"H\", \"1\", \"11.894477\", \"1.067495\", \"0.3402\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_2\", \"5\", \"H\", \"2\", \"12.477479\", \"2.628325\", \"0.36424\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_3\", \"5\", \"H\", \"3\", \"10.788606\", \"2.144589\", \"0.481677\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_4\", \"5\", \"H\", \"4\", \"11.436128\", \"3.796387\", \"0.548744\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_5\", \"5\", \"H\", \"5\", \"10.045364\", \"3.762815\", \"0.619708\", \"FOOTBOTTOM\", \"0.65\", \"0.0\", \"0.0\", \"-0.7\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_6\", \"5\", \"H\", \"6\", \"9.757002\", \"5.234279\", \"0.726518\", \"FOOTBOTTOM\", \"0.5\", \"0.0\", \"0.0\", \"-0.6\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_7\", \"5\", \"H\", \"7\", \"8.955986\", \"4.373268\", \"0.739376\", \"FOOTBOTTOM\", \"0.5\", \"0.0\", \"0.0\", \"-0.6\", \"Bottom\", \"Plantar\", \"Yes\"], [\"5_H_8\", \"5\", \"H\", \"8\", \"8.774654\", \"5.388553\", \"0.823411\", \"FOOTBOTTOM\", \"0.5\", \"0.0\", \"0.0\", \"-0.6\", \"Bottom\", \"Plantar\", \"Yes\"]],\n",
" 'settings': {}\n",
" }\n",
"\n",
" var dm, ec;\n",
"\n",
" function init() {\n",
" // Initialize the DecompositionModel\n",
" dm = new DecompositionModel('', data['sample_ids'],\n",
" data['coordinates'],\n",
" data['percents_explained'],\n",
" data['metadata_headers'], data['metadata'],\n",
" data['axes_names']);\n",
" // Initialize the EmperorController\n",
" ec = new EmperorController(dm, \"emperor-notebook-0x8db74d51\");\n",
" }\n",
"\n",
" function animate() {\n",
" requestAnimationFrame(animate);\n",
" ec.render();\n",
" }\n",
" $(window).resize(function() {\n",
" ec.resize(div.innerWidth(), div.innerHeight());\n",
" });\n",
"\n",
" $(function(){\n",
" init();\n",
" animate();\n",
"\n",
" ec.ready = function () {\n",
" // any other code that needs to be executed when emperor is loaded should\n",
" // go here\n",
" ec.loadConfig(data['settings']);\n",
" }\n",
" });\n",
"\n",
"}); // END REQUIRE.JS block\n",
"</script>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"<emperor.core.Emperor at 0x121785ac8>"
]
},
"execution_count": 59,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from emperor import Emperor\n",
"\n",
"mf = load_mf('annotation-man.tsv')\n",
"\n",
"dm = DistanceMatrix(scipy.spatial.distance.pdist(table.values, metric='jaccard'),\n",
" table.index.tolist())\n",
"Emperor(pcoa(dm), mf)"
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/yoshikivazquezbaeza/miniconda/envs/3mperor/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:102: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.3131840520542888 and the largest is 5.752519145447143.\n",
" RuntimeWarning\n"
]
}
],
"source": [
"dm = DistanceMatrix(scipy.spatial.distance.pdist(table.values, metric='braycurtis'),\n",
" table.index.tolist())\n",
"with open('braycurtis.index.lcms.html', 'w') as f:\n",
" f.write(str(Emperor(pcoa(dm), mf)))\n",
"\n",
"dm = DistanceMatrix(scipy.spatial.distance.pdist(table.values, metric='jaccard'),\n",
" table.index.tolist())\n",
"with open('jaccard.index.lcms.html', 'w') as f:\n",
" f.write(str(Emperor(pcoa(dm), mf)))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.5.1"
},
"widgets": {
"state": {},
"version": "1.1.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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