new-api.ipynb

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    "# 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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   "source": [
    "import pandas as pd, numpy as np\n",
    "from emperor import Emperor\n",
    "from skbio.stats.ordination import OrdinationResults\n",
    "\n",
    "\n",
    "from emperor.util import nbinstall"
   ]
  },
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   "cell_type": "markdown",
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   "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:"
   ]
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   "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",
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   "source": [
    "Before we can use this mapping file in Emperor, we should set the index\n",
    "    to be `SampleID`."
   ]
  },
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   "cell_type": "code",
   "execution_count": 3,
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   "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": {
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   "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": [],
   "source": [
    "x = Emperor(ores, mf, remote=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
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   "outputs": [
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       "  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",
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       "  function init() {\n",
       "    // Initialize the DecompositionModel\n",
       "    dm = new DecompositionModel(name, ids, coords, pct_var,\n",
       "                                md_headers, metadata);\n",
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