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ElDeveloper/Emperor Demo.ipynb

Created July 20, 2014 19:01
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Emperor Demo.ipynb
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"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"from skbio.math.stats.ordination import OrdinationResults\n",
"from qiime.parse import parse_mapping_file\n",
"from emperor import Emperor\n",
"\n",
"import numpy as np\n",
"\n",
"data, headers, _ = parse_mapping_file(open('/Users/yoshikivazquezbaeza/Downloads/'\n",
" 'processed_qiime_tutorial/Fasting_Map.txt', 'U'))\n",
"\n",
"ordination = OrdinationResults.from_file('/Users/yoshikivazquezbaeza/Downloads/'\n",
" 'processed_qiime_tutorial/wf_bdiv_even146/skbio.unweighted_unifrac_dm.txt')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 12
},
{
"cell_type": "code",
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"input": [
"p = Emperor(ordination, data, headers)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 13
},
{
"cell_type": "code",
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"input": [
"p"
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"language": "python",
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"outputs": [
{
"html": [
"<!doctype html>\n",
"<html lang=\"en\">\n",
"\n",
"<head>\n",
" <title>Emperor</title>\n",
" <meta charset=\"utf-8\">\n",
" <link rel=\"shortcut icon\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/img/favicon.ico\" />\n",
" <meta name=\"viewport\" content=\"width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0\">\n",
" <link rel=\"stylesheet\" type=\"text/css\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/emperor/css/emperor.css\">\n",
" <link rel=\"stylesheet\" type=\"text/css\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/css/jquery-ui2.css\">\n",
" <link rel=\"stylesheet\" type=\"text/css\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/css/colorPicker.css\">\n",
" <link rel=\"stylesheet\" type=\"text/css\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/css/spectrum.css\">\n",
" <link rel=\"stylesheet\" type=\"text/css\" href=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/css/d3.parcoords.css\">\n",
" <table id=\"logotable\" style=\"vertical-align:middle;text-align:center;height:100%;width:100%;margin:0;padding:0;border:0;\">\n",
" <tr><td><img src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/img/emperor.png\" alt=\"Emperor\" id=\"logo\"/></td></tr>\n",
" </table>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/d3.v3.min.js\"></script>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/d3.parcoords.js\"></script>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/jquery-1.7.1.min.js\"></script>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/jquery-ui-1.8.17.custom.min.js\"></script>\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/jquery.colorPicker.js\"></script>\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/spectrum.js\"></script>\n",
"\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/Three.js\"></script>\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/js/Detector.js\"></script>\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/js/RequestAnimationFrame.js\"></script>\n",
" <script src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/emperor/js/emperor.js\"></script>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/THREEx.screenshot.js\"></script>\n",
" <script type=\"text/javascript\" src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/js/FileSaver.min.js\"></script>\n",
" \n",
" <script type=\"text/javascript\">\n",
" \n",
"\n",
"var g_mappingFileHeaders = ['SampleID','BarcodeSequence','LinkerPrimerSequence','Treatment','DOB','Description'];\n",
"var g_mappingFileData = { 'PC.636': ['PC.636','ACGGTGAGTGTC','YATGCTGCCTCCCGTAGGAGT','Fast','20080116','Fasting_mouse_I.D._636'],'PC.355': ['PC.355','AACTCGTCGATG','YATGCTGCCTCCCGTAGGAGT','Control','20061218','Control_mouse_I.D._355'],'PC.607': ['PC.607','AACTGTGCGTAC','YATGCTGCCTCCCGTAGGAGT','Fast','20071112','Fasting_mouse_I.D._607'],'PC.634': ['PC.634','ACAGAGTCGGCT','YATGCTGCCTCCCGTAGGAGT','Fast','20080116','Fasting_mouse_I.D._634'],'PC.635': ['PC.635','ACCGCAGAGTCA','YATGCTGCCTCCCGTAGGAGT','Fast','20080116','Fasting_mouse_I.D._635'],'PC.593': ['PC.593','AGCAGCACTTGT','YATGCTGCCTCCCGTAGGAGT','Control','20071210','Control_mouse_I.D._593'],'PC.356': ['PC.356','ACAGACCACTCA','YATGCTGCCTCCCGTAGGAGT','Control','20061126','Control_mouse_I.D._356'],'PC.481': ['PC.481','ACCAGCGACTAG','YATGCTGCCTCCCGTAGGAGT','Control','20070314','Control_mouse_I.D._481'],'PC.354': ['PC.354','AGCACGAGCCTA','YATGCTGCCTCCCGTAGGAGT','Control','20061218','Control_mouse_I.D._354'] };\n",
"\n",
"\n",
"var g_spherePositions = new Array();\n",
"g_spherePositions['PC.354'] = { 'name': 'PC.354', 'color': 0, 'x': -0.276542, 'y': -0.144964, 'z': 0.066647, 'P1': -0.276542, 'P2': -0.144964, 'P3': 0.066647, 'P4': -0.067711, 'P5': 0.176070, 'P6': 0.072969, 'P7': -0.229889, 'P8': -0.046599 };\n",
"g_spherePositions['PC.355'] = { 'name': 'PC.355', 'color': 0, 'x': -0.237661, 'y': 0.046053, 'z': -0.138136, 'P1': -0.237661, 'P2': 0.046053, 'P3': -0.138136, 'P4': 0.159061, 'P5': -0.247485, 'P6': -0.115211, 'P7': -0.112864, 'P8': 0.064794 };\n",
"g_spherePositions['PC.356'] = { 'name': 'PC.356', 'color': 0, 'x': 0.228820, 'y': -0.130142, 'z': -0.287149, 'P1': 0.228820, 'P2': -0.130142, 'P3': -0.287149, 'P4': 0.086450, 'P5': 0.044295, 'P6': 0.206043, 'P7': 0.031000, 'P8': 0.071992 };\n",
"g_spherePositions['PC.481'] = { 'name': 'PC.481', 'color': 0, 'x': 0.042263, 'y': -0.013968, 'z': 0.063531, 'P1': 0.042263, 'P2': -0.013968, 'P3': 0.063531, 'P4': -0.346121, 'P5': -0.127814, 'P6': 0.013935, 'P7': 0.030021, 'P8': 0.140148 };\n",
"g_spherePositions['PC.593'] = { 'name': 'PC.593', 'color': 0, 'x': 0.280399, 'y': -0.006013, 'z': 0.023485, 'P1': 0.280399, 'P2': -0.006013, 'P3': 0.023485, 'P4': -0.046811, 'P5': -0.146624, 'P6': 0.005670, 'P7': -0.035430, 'P8': -0.255786 };\n",
"g_spherePositions['PC.607'] = { 'name': 'PC.607', 'color': 0, 'x': 0.232873, 'y': 0.139788, 'z': 0.322871, 'P1': 0.232873, 'P2': 0.139788, 'P3': 0.322871, 'P4': 0.183347, 'P5': 0.020466, 'P6': 0.054059, 'P7': -0.036625, 'P8': 0.099824 };\n",
"g_spherePositions['PC.634'] = { 'name': 'PC.634', 'color': 0, 'x': 0.170518, 'y': -0.194113, 'z': -0.030897, 'P1': 0.170518, 'P2': -0.194113, 'P3': -0.030897, 'P4': 0.019809, 'P5': 0.155100, 'P6': -0.279924, 'P7': 0.057609, 'P8': 0.024248 };\n",
"g_spherePositions['PC.635'] = { 'name': 'PC.635', 'color': 0, 'x': -0.091330, 'y': 0.424147, 'z': -0.135627, 'P1': -0.091330, 'P2': 0.424147, 'P3': -0.135627, 'P4': -0.057519, 'P5': 0.151363, 'P6': -0.025394, 'P7': 0.051731, 'P8': -0.038738 };\n",
"g_spherePositions['PC.636'] = { 'name': 'PC.636', 'color': 0, 'x': -0.349339, 'y': -0.120788, 'z': 0.115275, 'P1': -0.349339, 'P2': -0.120788, 'P3': 0.115275, 'P4': 0.069495, 'P5': -0.025372, 'P6': 0.067853, 'P7': 0.244448, 'P8': -0.059883 };\n",
"\n",
"var g_ellipsesDimensions = new Array();\n",
"var g_segments = 8, g_rings = 8, g_radius = 0.007557;\n",
"var g_xAxisLength = 0.629738;\n",
"var g_yAxisLength = 0.618260;\n",
"var g_zAxisLength = 0.610021;\n",
"var g_xMaximumValue = 0.280399;\n",
"var g_yMaximumValue = 0.424147;\n",
"var g_zMaximumValue = 0.322871;\n",
"var g_xMinimumValue = -0.349339;\n",
"var g_yMinimumValue = -0.194113;\n",
"var g_zMinimumValue = -0.287149;\n",
"var g_maximum = 0.424147;\n",
"var g_pc1Label = \"PC1 (0.27 %)\";\n",
"var g_pc2Label = \"PC2 (0.16 %)\";\n",
"var g_pc3Label = \"PC3 (0.14 %)\";\n",
"var g_number_of_custom_axes = 0;\n",
"var g_fractionExplained = [0.002669, 0.001626, 0.001378, 0.001122, 0.001002, 0.000823, 0.000756, 0.000625];\n",
"var g_fractionExplainedRounded = [0.27, 0.16, 0.14, 0.11, 0.10, 0.08, 0.08, 0.06];\n",
"\n",
"\n",
"var g_taxaPositions = new Array();\n",
"\n",
"\n",
"\n",
"var g_comparisonPositions = new Array();\n",
"var g_isSerialComparisonPlot = true;\n",
"\n",
"\n",
"var g_vectorPositions = new Array();\n",
"\n",
"document.getElementById(\"logo\").style.display = 'none';\n",
"document.getElementById(\"logotable\").style.display = 'none';\n",
"\n",
" </script>\n",
"</head>\n",
"\n",
"<body>\n",
"\n",
"<div id=\"overlay\">\n",
" <div>\n",
" <img src=\"http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources/img/emperor.png\" alt=\"Emperor\" id=\"small-logo\"/>\n",
" <h1>WebGL is not enabled!</h1>\n",
" <p>Emperor's visualization framework is WebGL based, it seems that your system doesn't have this resource available. Here is what you can do:</p>\n",
" <p id=\"explanation\"><strong>Chrome:</strong> Type \"chrome://flags/\" into the address bar, then search for \"Disable WebGL\". Disable this option if you haven't already. <em>Note:</em> If you follow these steps and still don't see an image, go to \"chrome://flags/\" and then search for \"Override software rendering list\" and enable this option.</p>\n",
" <p id=\"explanation\"><strong>Safari:</strong> Open Safari's menu and select Preferences. Click on the advanced tab, and then check \"Show Developer\" menu. Then open the \"Developer\" menu and select \"Enable WebGL\".</p>\n",
" <p id=\"explanation\"><strong>Firefox:</strong> Go to Options through Firefox > Options or Tools > Options. Go to Advanced, then General. Check \"Use hardware acceleration when available\" and restart Firefox.</p>\n",
" <p id=\"explanation\"><strong>Other browsers:</strong> The only browsers that support WebGL are Chrome, Safari, and Firefox. Please switch to these browsers when using Emperor.</p>\n",
" <p id=\"explanation\"><em>Note:</em> Once you went through these changes, reload the page and it should work!</p>\n",
" <p id=\"source\">Sources: Instructions for <a href=\"https://www.biodigitalhuman.com/home/enabling-webgl.html\">Chrome and Safari</a>, and <a href=\"http://www.infewbytes.com/?p=144\">Firefox</a></p>\n",
" </div>\n",
"</div>\n",
"\n",
"<div id=\"emperor-plot-toggle\">\n",
" <form>\n",
" <div id=\"plottype\">\n",
" <input id=\"pcoa\" type=\"radio\" id=\"pcoa\" name=\"plottype\" checked=\"checked\" /><label for=\"pcoa\">PCoA</label>\n",
" <input id=\"parallel\" type=\"radio\" id=\"parallel\" name=\"plottype\" /><label for=\"parallel\">Parallel</label>\n",
" </div>\n",
" </form>\n",
"</div>\n",
"<div id=\"pcoaPlotWrapper\" class=\"emperor-plot-wrapper\">\n",
" <label id=\"pointCount\" class=\"ontop\">\n",
" </label>\n",
"\n",
" <div id=\"finder\" class=\"arrow-right\">\n",
" </div>\n",
"\n",
" <div id=\"labels\" class=\"unselectable\">\n",
" </div>\n",
"\n",
" <div id=\"taxalabels\" class=\"unselectable\">\n",
" </div>\n",
"\n",
" <div id=\"axislabels\" class=\"axis-labels\">\n",
" </div>\n",
"\n",
" <div id=\"main-plot\">\n",
" </div>\n",
"</div>\n",
"\n",
"<div id=\"parallelPlotWrapper\" class=\"emperor-plot-wrapper\">\n",
"</div>\n",
"\n",
"<div id=\"emperor-separator\" class=\"emperor-separator\" ondblclick=\"separatorDoubleClick()\"></div>\n",
"\n",
"<div id=\"emperor-menu\">\n",
" <div id=\"emperor-menu-tabs\">\n",
" <ul>\n",
" <li><a href=\"#keytab\">Key</a></li>\n",
" <li><a href=\"#colorby\">Colors</a></li>\n",
" <li><a href=\"#showby\">Visibility</a></li>\n",
" <li><a href=\"#scalingby\">Scaling</a></li>\n",
" <li><a href=\"#labelby\">Labels</a></li>\n",
" <li><a href=\"#axes\">Axes</a></li>\n",
" <li><a href=\"#options\">Options</a></li>\n",
" </ul>\n",
" <div id=\"keytab\" class=\"emperor-tab-div\">\n",
" <form name=\"keyFilter\">\n",
" <label>Filter </label><input name=\"filterBox\" id=\"searchBox\" type=\"text\" onkeyup=\"filterKey()\"></input>\n",
" </form>\n",
" <div id=\"key\">\n",
" </div>\n",
" </div>\n",
" <div id=\"colorby\" class=\"emperor-tab-div\">\n",
" <input type=\"checkbox\" onchange=\"toggleContinuousAndDiscreteColors(this)\" id=\"discreteorcontinuouscolors\" name=\"discreteorcontinuouscolors\"> Use gradient colors</input>\n",
" <br><br>\n",
" <select id=\"colorbycombo\" onchange=\"colorByMenuChanged()\" size=\"3\" class=\"emperor-tab-drop-down\">\n",
" </select>\n",
" <div class=\"list\" id=\"colorbylist\">\n",
" </div>\n",
" </div>\n",
" <div id=\"showby\" class=\"emperor-tab-div\">\n",
" <table class=\"emperor-tab-table\">\n",
" <tr>\n",
" <td align=\"center\">\n",
" <select id=\"showbycombo\" onchange=\"showByMenuChanged()\" class=\"emperor-tab-drop-down\">\n",
" </select>\n",
" </td>\n",
" </tr>\n",
" <tr>\n",
" <td>\n",
" <div class=\"list\" id=\"showbylist\" style=\"height:100%%;width:100%%\">\n",
" </div>\n",
" </td>\n",
" </tr>\n",
" <tr>\n",
" <td style=\"padding-left: 12px; padding-right:12px;\">\n",
" <hr class='section-break'>\n",
" <br>\n",
" <label for=\"sphereopacity\" class=\"text\">Global Sphere Opacity</label>\n",
" <label id=\"sphereopacity\" class=\"slidervalue\"></label>\n",
" <div id=\"sopacityslider\" class=\"slider-range-max\"></div>\n",
" </td>\n",
" </tr>\n",
" <tr>\n",
" <td align=\"center\">\n",
" <button id=\"toggle-visibility-selection-button\" onClick=\"toggleVisibleCategories()\">Invert Selected</button>\n",
" </td>\n",
" </tr>\n",
" </table>\n",
" </div>\n",
" <div id=\"scalingby\" class=\"emperor-tab-div\">\n",
" <table class=\"emperor-tab-table\">\n",
" <tr>\n",
" <td align=\"center\">\n",
" <select id=\"scalingbycombo\" onchange=\"scalingByMenuChanged()\" class=\"emperor-tab-drop-down\">\n",
" </select>\n",
" </td>\n",
" </tr>\n",
" <tr>\n",
" <td>\n",
" <div class=\"list\" id=\"scalingbylist\" style=\"height:100%%;width:100%%\">\n",
" </div>\n",
" </td>\n",
" </tr>\n",
" <tr>\n",
" <td style=\"padding-left: 12px; padding-right:12px;\">\n",
" <hr class='section-break'>\n",
" <br>\n",
" <label for=\"sphereradius\" class=\"text\">Global Sphere Scale</label>\n",
" <label id=\"sphereradius\" class=\"slidervalue\"></label>\n",
" <div id=\"sradiusslider\" class=\"slider-range-max\"></div>\n",
" </td>\n",
" </tr>\n",
" </table>\n",
" </div>\n",
" <div id=\"labelby\" class=\"emperor-tab-div\">\n",
" <div id=\"labels-top\">\n",
" <form name=\"plotoptions\">\n",
" <input type=\"checkbox\" onClick=\"toggleLabels()\">Samples Label Visibility</input>\n",
" </form>\n",
" <br>\n",
" <label for=\"labelopacity\" class=\"text\">Label Opacity</label>\n",
" <label id=\"labelopacity\" class=\"slidervalue\"></label>\n",
" <div id=\"lopacityslider\" class=\"slider-range-max\"></div>\n",
" <div id=\"label-color-holder clearfix\">\n",
" <table class=\"emperor-tab-table\">\n",
" <tr><td><div id=\"labelColor\" class=\"colorbox\"></div></td><td><label>Master Label Color</label></td></tr>\n",
" <br><br>\n",
" </table></div>\n",
" </div>\n",
" <br>\n",
" <select id=\"labelcombo\" onchange=\"labelMenuChanged()\" class=\"emperor-tab-drop-down\">\n",
" </select>\n",
" <div class=\"list\" id=\"label-list\">\n",
" </div>\n",
" </div>\n",
" <div id=\"axes\" class=\"emperor-tab-div\">\n",
" <div id=\"pcoaaxes\">\n",
" <div class=\"list\" id=\"axeslist\">\n",
" </div>\n",
" </div>\n",
" </div>\n",
" <div id=\"options\" class=\"emperor-tab-div\">\n",
" <table class=\"emperor-tab-table\">\n",
" <tr><td><div id=\"axeslabelscolor\" class=\"colorbox\" name=\"axeslabelscolor\"></div></td><td title=\"Axes Labels Color\">Axes Labels Color</td></tr>\n",
" <tr><td><div id=\"axescolor\" class=\"colorbox\" name=\"axescolor\"></div></td><td title=\"Axes Color Title\">Axes Color</td></tr>\n",
" <tr><td><div id=\"rendererbackgroundcolor\" class=\"colorbox\" name=\"rendererbackgroundcolor\"></div></td><td title=\"Background Color Title\">Background Color</td></tr>\n",
" <tr><td colspan=\"2\">\n",
" <div id=\"pcoaviewoptions\" class=\"\">\n",
" <form name=\"settingsoptionscolor\">\n",
" </form>\n",
" <div id=\"pcoaoptions\" class=\"\">\n",
" <form name=\"settingsoptions\">\n",
" <input type=\"checkbox\" onchange=\"toggleScaleCoordinates(this)\" id=\"scale_checkbox\" name=\"scale_checkbox\">Scale coords by percent explained</input>\n",
" </form>\n",
" </div>\n",
" <br><input id=\"reset\" class=\"button\" type=\"submit\" value=\"Recenter Camera\" style=\"\" onClick=\"resetCamera()\">\n",
" <br><br>\n",
" <hr class='section-break'>\n",
" <br>Filename <small>(only letters, numbers, ., - and _)</small>:\n",
" <br><input name=\"saveas_name\" id=\"saveas_name\" value=\"screenshot\" type=\"text\"/>\n",
" <br><input id=\"saveas_legends\" class=\"checkbox\" type=\"checkbox\" style=\"\"> Create legend\n",
" <input id=\"saveas\" class=\"button\" type=\"submit\" value=\"Save as SVG\" style=\"\" onClick=\"saveSVG()\"/>\n",
" <br><br>For a PNG, simply press 'ctrl+p'.\n",
" <div id=\"paralleloptions\" class=\"\">\n",
" </div>\n",
" </div>\n",
" <br>\n",
" </td></tr>\n",
" </table>\n",
" </div>\n",
" </div> \n",
"</div>\n",
"</body>\n",
"\n",
"</html>\n"
],
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{
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"text": [
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}
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