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ElDeveloper/embedded_figure_1.ipynb

Created December 11, 2017 23:23
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embedded_figure_1.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Embedded Figure 1 from \"Deblur rapidly resolves single-nucleotide community sequence patterns\" showing merged _de novo_ OTU picking runs. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pandas as pd\n",
"import skbio\n",
"from emperor import Emperor, nbinstall\n",
"nbinstall()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"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/1.0.0-beta.7/emperor/support_files/css/emperor.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/jquery-ui.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/slick.grid.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/spectrum.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/chosen.min.css\">',\n",
" '<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/css/jquery.contextMenu.min.css\">'\n",
" ]);\n",
"}}\n",
"</script>\n",
"\n",
"<div id='emperor-notebook-0x2149b97f' 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/1.0.0-beta.7/emperor/support_files/img/emperor.png' alt='Emperor resources missing. Expected them to be found in https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/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/1.0.0-beta.7/emperor/support_files/vendor/js/jquery-2.1.4.min',\n",
" 'jqueryui': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery-ui.min',\n",
" 'jquery_drag': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.event.drag-2.2.min',\n",
"\n",
" /* jQuery plugins */\n",
" 'chosen': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/chosen.jquery.min',\n",
" 'spectrum': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/spectrum.min',\n",
" 'position': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.ui.position.min',\n",
" 'contextmenu': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/jquery.contextMenu.min',\n",
"\n",
" /* other libraries */\n",
" 'underscore': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/underscore-min',\n",
" 'chroma': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/chroma.min',\n",
" 'filesaver': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/FileSaver.min',\n",
" 'blob': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/Blob',\n",
" 'canvastoblob': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/canvas-toBlob',\n",
" 'd3': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/d3.min',\n",
"\n",
" /* THREE.js and plugins */\n",
" 'three': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.min',\n",
" 'orbitcontrols': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/OrbitControls',\n",
" 'projector': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/Projector',\n",
" 'svgrenderer': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/SVGRenderer',\n",
" 'canvasrenderer': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/three.js-plugins/CanvasRenderer',\n",
"\n",
" /* SlickGrid */\n",
" 'slickcore': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.core.min',\n",
" 'slickgrid': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.grid.min',\n",
" 'slickformatters': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.editors.min',\n",
" 'slickeditors': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/vendor/js/slick.formatters.min',\n",
"\n",
" /* Emperor's objects */\n",
" 'util': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/util',\n",
" 'model': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/model',\n",
" 'view': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/view',\n",
" 'controller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/controller',\n",
" 'draw': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/draw',\n",
" 'scene3d': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/sceneplotview3d',\n",
" 'abcviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/abc-view-controller',\n",
" 'viewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/view-controller',\n",
" 'colorviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/color-view-controller',\n",
" 'visibilitycontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/visibility-controller',\n",
" 'scaleviewcontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/scale-view-controller',\n",
" 'shapecontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/shape-controller',\n",
" 'axescontroller': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/axes-controller',\n",
" 'shape-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/shape-editor',\n",
" 'color-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/color-editor',\n",
" 'scale-editor': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/emperor/support_files/js/scale-editor',\n",
" 'shapes': 'https://cdn.rawgit.com/biocore/emperor/1.0.0-beta.7/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",
" 'orbitcontrols': {\n",
" 'deps': ['three']\n",
" },\n",
" 'projector': {\n",
" 'deps': ['three']\n",
" },\n",
" 'svgrenderer': {\n",
" 'deps': ['orbitcontrols', 'projector']\n",
" },\n",
" 'canvasrenderer': {\n",
" 'deps': ['orbitcontrols', 'projector']\n",
" },\n",
"'slickcore': ['jqueryui'],\n",
"'slickgrid': ['slickcore', 'jquery_drag', 'slickformatters',\n",
" '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-0x2149b97f');\n",
"\n",
" var data = {\n",
" // coordinates information\n",
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" 'axes_names': [0, 1, 2, 3, 4],\n",
" 'percents_explained': [3.9310348878299997, 3.9079440139300003, 3.19599122527, 2.7754763199299997, 2.37033248935],\n",
"\n",
" // sample information\n",
" 'metadata_headers': [\"SampleID\", \"VIOSCREEN_MANNITOL\", \"VIOSCREEN_SFA100\", \"NON_FOOD_ALLERGIES_BEESTINGS\", \"VIOSCREEN_FINISHED\", \"TONSILS_REMOVED\", \"VIOSCREEN_SFA170\", \"VIOSCREEN_VEGETABLE_SERVINGS\", \"VIOSCREEN_SORBITOL\", \"COUNTRY_OF_BIRTH\", \"PETS_OTHER\", \"ECONOMIC_REGION\", \"VIOSCREEN_SFA80\", \"VIOSCREEN_BETACAR\", \"CANCER_TREATMENT\", \"VIOSCREEN_LOW_FAT_DAIRY_SERVING\", \"VIOSCREEN_NIACINEQ\", \"LinkerPrimerSequence\", \"VIOSCREEN_GAMMTOCO\", \"VIOSCREEN_LYSINE\", \"VIOSCREEN_ISOMALT\", \"LIVER_DISEASE\", \"BODY_PRODUCT\", \"VIOSCREEN_DATABASE\", \"ARTIFICIAL_SWEETENERS\", \"VIOSCREEN_SUCROSE\", \"ENA-BASE-COUNT\", \"VIOSCREEN_CLAC9T11\", \"SUBSET_HEALTHY\", \"VIOSCREEN_FIBER\", \"VIOSCREEN_LACTITOL\", \"VIOSCREEN_HEI_NON_JUICE_FRT\", \"CONTRACEPTIVE\", \"ALLERGIC_TO_UNSPECIFIED\", \"VIOSCREEN_OXALICM\", \"VIOSCREEN_ALPHACAR\", \"SALTED_SNACKS_FREQUENCY\", \"ALCOHOL_TYPES_UNSPECIFIED\", \"AGE_CAT\", \"VIOSCREEN_LYCOPENE\", \"VIOSCREEN_VEG5_DAY\", 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\"VIOSCREEN_WHOLE_GRAIN_SERVINGS\", \"VIOSCREEN_HEI2010_PROTIEN_FOODS\", \"ENV_FEATURE\", \"NAIL_BITER\", \"VIOSCREEN_NCCGLGR\", \"VIOSCREEN_OXALIC\", \"VIOSCREEN_HEI_FRUIT\", \"VIOSCREEN_QUESTIONNAIRE\", \"VITAMIN_D_SUPPLEMENT_FREQUENCY\", \"ADD_ADHD\", \"READY_TO_EAT_MEALS_FREQUENCY\", \"VIOSCREEN_MFA161\", \"VIOSCREEN_SATOCO\", \"VIOSCREEN_RIBOFLA\", \"VIOSCREEN_STARCH\", \"VIOSCREEN_MFA221\", \"IBD\", \"CAT\", \"HOST_TAXID\", \"VIOSCREEN_V_TOTAL\", \"VIOSCREEN_V_ORANGE\", \"IBS\", \"VIOSCREEN_M_FRANK\", \"COLLECTION_TIMESTAMP\", \"VIOSCREEN_DELTTOCO\", \"MULTIVITAMIN\", \"CANCER\", \"ACNE_MEDICATION_OTC\", \"VIOSCREEN_FRUIT_SERVINGS\", \"ALLERGIC_TO_I_HAVE_NO_FOOD_ALLERGIES_THAT_I_KNOW_OF\", \"DIABETES\", \"CDIFF\", \"MENTAL_ILLNESS_TYPE_BIPOLAR_DISORDER\", \"ALLERGIC_TO_OTHER\", \"VIOSCREEN_BETATOCO\", \"HEIGHT_CM\", \"VIOSCREEN_FRIED_FOOD_SERVINGS\", \"VIOSCREEN_FISH_SERVINGS\", \"CHICKENPOX\", \"VIOSCREEN_FRTSUMM\", \"VIOSCREEN_GRAMS\", \"ASSIGNED_FROM_GEO\", 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