EMPeror Demo.ipynb

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# using the formatters in Emperor\n",
      "from emperor.format import (format_mapping_file_to_js, format_pcoa_to_js,\n",
      "                            format_taxa_to_js, format_vectors_to_js,\n",
      "                            format_comparison_bars_to_js, EMPEROR_HEADER_HTML_STRING,\n",
      "                            format_emperor_html_footer_string)\n",
      "\n",
      "# we are going to use this remote location to load resources\n",
      "resources_url = 'http://emperor.colorado.edu/master/make_emperor/emperor_output/emperor_required_resources'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from skbio.maths.stats.ordination import PCoA\n",
      "from skbio.core.distance import SymmetricDistanceMatrix, DistanceMatrix\n",
      "import numpy as np"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from qiime.parse import parse_mapping_file\n",
      "data, headers, _ = parse_mapping_file(open('Fasting_Map.txt', 'U'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "dm = SymmetricDistanceMatrix.from_file(open('unweighted_unifrac_dm.txt', 'U'))\n",
      "pcoa = PCoA(dm)\n",
      "\n",
      "# grab the things we need for the plot\n",
      "coords = pcoa.scores().species\n",
      "eigvals = pcoa.scores().eigvals\n",
      "pcts = np.ones(len(eigvals))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# i am assuming the order from the dm to the PCoA object is preserved\n",
      "pcoa_string = format_pcoa_to_js(dm.ids, coords, eigvals, pcts)\n",
      "mf_string = format_mapping_file_to_js(data, headers, headers)\n",
      "\n",
      "# A lot of this is going to be empty because we don't really need any of it\n",
      "footer = format_emperor_html_footer_string(False, False, False, False)\n",
      "taxa = format_taxa_to_js([], [], [])\n",
      "bars = format_comparison_bars_to_js([], [], 0)\n",
      "vectors = format_vectors_to_js([], [], [], [], None)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from IPython.display import HTML, IFrame"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# build the HTML string\n",
      "output = [EMPEROR_HEADER_HTML_STRING,\n",
      "          mf_string,\n",
      "          pcoa_string,\n",
      "          taxa,\n",
      "          bars,\n",
      "          vectors,\n",
      "          footer]\n",
      "# add the remote resources\n",
      "output = '\\n'.join(output).replace('emperor_required_resources', resources_url)\n",
      "\n",
      "fd = open('d.html', 'w')\n",
      "fd.write(output)\n",
      "fd.close()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "IFrame('files/d.html', 800, 400)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "\n",
        "        <iframe\n",
        "            width=\"800\"\n",
        "            height=400\"\n",
        "            src=\"files/d.html\"\n",
        "            frameborder=\"0\"\n",
        "            allowfullscreen\n",
        "        ></iframe>\n",
        "        "
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 9,
       "text": [
        "<IPython.lib.display.IFrame at 0x10820bb90>"
       ]
      }
     ],
     "prompt_number": 9
    }
   ],
   "metadata": {}
  }
 ]
}