new-api.ipynb

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   "source": [
    "# Emperor's Python API\n",
    "\n",
    "**This notebook demonstrate Emperor's new Python API, which can and will change as we continue to exercise this interface, for more information, have a look at the [pull request here](https://github.com/biocore/emperor/pull/452).**"
   ]
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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
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   "outputs": [],
   "source": [
    "import pandas as pd, numpy as np\n",
    "from emperor import Emperor\n",
    "from skbio.stats.ordination import OrdinationResults"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Ordination plots are almost invariantly associated with a set of data, that\n",
    "    relates each sample to its scientific context, we refer to this as the\n",
    "    *sample metadata*, and represent it using Pandas `DataFrame`s. For this\n",
    "    example we will need some metadata, we start by creating our metadata\n",
    "    object:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "data = [['PC.354', 'Control', '20061218', 'Control_mouse_I.D._354'],\n",
    "['PC.355', 'Control', '20061218', 'Control_mouse_I.D._355'],\n",
    "['PC.356', 'Control', '20061126', 'Control_mouse_I.D._356'],\n",
    "['PC.481', 'Control', '20070314', 'Control_mouse_I.D._481'],\n",
    "['PC.593', 'Control', '20071210', 'Control_mouse_I.D._593'],\n",
    "['PC.607', 'Fast', '20071112', 'Fasting_mouse_I.D._607'],\n",
    "['PC.634', 'Fast', '20080116', 'Fasting_mouse_I.D._634'],\n",
    "['PC.635', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],\n",
    "['PC.636', 'Fast', '20080116', 'Fasting_mouse_I.D._636']]\n",
    "columns = ['SampleID', 'Treatment', 'DOB', 'Description']\n",
    "mf = pd.DataFrame(columns=columns, data=data)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Before we can use this mapping file in Emperor, we should set the index\n",
    "    to be `SampleID`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mf.set_index('SampleID', inplace=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then let's create some artificial ordination data, and encapsulate it in an `OrdinationResults` object:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "eigvals = np.array([0.47941212, 0.29201496, 0.24744925,\n",
    "                    0.20149607, 0.18007613, 0.14780677,\n",
    "                    0.13579593, 0.1122597, 0.])\n",
    "n = eigvals.shape[0]\n",
    "site = np.random.randn(n, n)\n",
    "site_ids = ('PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593',\n",
    "            'PC.355', 'PC.607', 'PC.634')\n",
    "p_explained = np.array([0.26688705, 0.1625637, 0.13775413, 0.11217216,\n",
    "                     0.10024775, 0.08228351, 0.07559712, 0.06249458,\n",
    "                     0.])\n",
    "ores = OrdinationResults(eigvals, site=site, site_ids=site_ids,\n",
    "                         proportion_explained=p_explained)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally import the Emperor object and display it using Jupyter:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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       "<script type=\"text/javascript\">\n",
       "\n",
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       "\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",
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       "<div id='python-penguin' style=\"position: relative; width:100%; height:500px;\"></div>\n",
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       "requirejs.config({\n",
       "'baseUrl': 'https://cdn.rawgit.com/biocore/emperor/new-api/emperor/support_files/',\n",
       "\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': './vendor/js/jquery-2.1.4.min',\n",
       "  'jqueryui': './vendor/js/jquery-ui.min',\n",
       "  'jquery_drag': './vendor/js/jquery.event.drag-2.2.min',\n",
       "\n",
       "  /* jQuery plugins */\n",
       "  'chosen': './vendor/js/chosen.jquery.min',\n",
       "  'spectrum': './vendor/js/spectrum.min',\n",
       "\n",
       "  /* other libraries */\n",
       "  'underscore': './vendor/js/underscore-min',\n",
       "  'chroma': './vendor/js/chroma.min',\n",
       "\n",
       "\n",
       "  /* THREE.js and plugins */\n",
       "  'three': './vendor/js/three.min',\n",
       "  'orbitcontrols': './vendor/js/three.js-plugins/OrbitControls',\n",
       "\n",
       "  /* SlickGrid */\n",
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       "  'slickgrid': './vendor/js/slick.grid.min',\n",
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       "  'slickeditors': './vendor/js/slick.formatters.min',\n",
       "\n",
       "  /* Emperor's objects */\n",
       "  'model': './js/model',\n",
       "  'view': './js/view',\n",
       "  'controller': './js/controller',\n",
       "  'draw': './js/draw',\n",
       "  'scene3d': './js/sceneplotview3d',\n",
       "  'viewcontroller': './js/view-controller',\n",
       "  'colorviewcontroller': './js/color-view-controller',\n",
       "  'visibilitycontroller': './js/visibility-controller',\n",
       "  'color-editor': './js/color-editor',\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",
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       "    'exports': 'jQuery.fn.chosen'\n",
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       "  'orbitcontrols': {\n",
       "    'deps': ['three']\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 = $('#python-penguin');\n",
       "  console.log(div)\n",
       "\n",
       "  var ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'];\n",
       "  var coords = [[-0.5418718907766492, -0.2322126893194602, -1.5539895843555012, 0.9779585378585399, 0.6042066278652377], [-0.2503362247947621, 0.8942067532695469, -1.0375639554615006, -0.9668682696455478, 1.2991267859486286], [-1.2200313367348732, 0.6643872498952018, -0.65388232100731, -2.345168064831795, 0.07365375267196608], [-1.299922446104461, -0.49940762996086824, -1.4588543159826317, -0.4581513497497899, -0.26903536762453084], [-0.4707135792295782, 0.6552745171213014, 0.5823626766059697, -1.3364612709123511, -0.766335524161582], [-0.049433459884668546, 1.0362826585877511, 0.8842607848886942, 1.2840369826241902, -1.6017134657210061], [1.1372013797254774, 0.24274217197919976, 0.7617551968188236, -0.13655232966645264, -0.006742256118561079], [-1.3895886254303131, 0.8943439629112457, -0.024193070133999576, -1.3511555607575463, -0.020358237939723352], [-0.19329959778688968, 0.6177460059036628, -0.6422863415264983, -0.4271313469417334, -0.4913303558720307]];\n",
       "  var pct_var = [0.26688705, 0.1625637, 0.13775413, 0.11217216, 0.10024775];\n",
       "  var md_headers = ['SampleID', 'Treatment', 'DOB', 'Description'];\n",
       "  var metadata = [['PC.636', 'Fast', '20080116', 'Fasting_mouse_I.D._636'], ['PC.635', 'Fast', '20080116', 'Fasting_mouse_I.D._635'], ['PC.356', 'Control', '20061126', 'Control_mouse_I.D._356'], ['PC.481', 'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.354', 'Control', '20061218', 'Control_mouse_I.D._354'], ['PC.593', 'Control', '20071210', 'Control_mouse_I.D._593'], ['PC.355', 'Control', '20061218', 'Control_mouse_I.D._355'], ['PC.607', 'Fast', '20071112', 'Fasting_mouse_I.D._607'], ['PC.634', 'Fast', '20080116', 'Fasting_mouse_I.D._634']];\n",
       "\n",
       "  var dm, ec;\n",
       "\n",
       "  function init() {\n",
       "    // Initialize the DecompositionModel\n",
       "    dm = new DecompositionModel(name, ids, coords, pct_var,\n",
       "                                md_headers, metadata);\n",
       "    // Initialize the EmperorController\n",
       "    ec = new EmperorController(dm, 'python-penguin');\n",
       "    lol = ec\n",
       "  }\n",
       "\n",
       "  function animate() {\n",
       "    requestAnimationFrame(animate);\n",
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       "  }\n",
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       "  });\n",
       "\n",
       "  $(function(){\n",
       "    init();\n",
       "    animate();\n",
       "\n",
       "  });\n",
       "\n",
       "}); // END REQUIRE.JS block\n",
       "</script>"
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       "<emperor.core.Emperor at 0x10a6b4810>"
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   ],
   "source": [
    "Emperor(ores, mf)"
   ]
  }
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