leo_fucci_es_rnaseq.ipynb

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import glob\n",
      "from itertools import combinations\n",
      "import os\n",
      "\n",
      "import pandas as pd\n",
      "from IPython.core.display import HTML\n",
      "import scipy.stats\n",
      "from gscripts.general import parsers\n",
      "\n",
      "analysis_dir = \"/nas3/gpratt/projects/leo/analysis/fucci_rnaseq_v1/\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "nrf_files = glob.glob(os.path.join(analysis_dir, \"*.NRF.metrics\"))\n",
      "nrf_frame = pd.DataFrame({\".\".join(os.path.basename(nrf_file).split(\".\")[0:2]) : \n",
      "                          parsers.parse_nrf_file(nrf_file) for nrf_file in nrf_files}).transpose()\n",
      "\n",
      "qc_files = glob.glob(os.path.join(analysis_dir, \"*.final.out\"))\n",
      "star_frame = pd.DataFrame({\".\".join(os.path.basename(qc_file).split(\".\")[0:2]) : \n",
      "                           parsers.parse_star_file(qc_file) for qc_file in qc_files}).transpose()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "combined_df = pd.merge(nrf_frame, star_frame, left_index=True, right_index=True, how=\"outer\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "HTML(combined_df.to_html(formatters={\"Number of input reads\" : parsers.commas,\n",
      "                             \"Uniquely mapped reads number\" : parsers.commas,\n",
      "                             \"Usable Reads\" : parsers.commas,\n",
      "                             \"Num Peaks\": parsers.commas,\n",
      "                             \"Trimmed reads\" : parsers.commas,\n",
      "                             \"Processed reads\" : parsers.commas,\n",
      "                             \"Too short reads\" : parsers.commas}))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<table border=\"1\" class=\"dataframe\">\n",
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>NRF</th>\n",
        "      <th>PCB</th>\n",
        "      <th>% of reads mapped to multiple loci</th>\n",
        "      <th>% of reads mapped to too many loci</th>\n",
        "      <th>% of reads unmapped: other</th>\n",
        "      <th>% of reads unmapped: too many mismatches</th>\n",
        "      <th>% of reads unmapped: too short</th>\n",
        "      <th>Average input read length</th>\n",
        "      <th>Average mapped length</th>\n",
        "      <th>Deletion average length</th>\n",
        "      <th>Deletion rate per base</th>\n",
        "      <th>Finished on</th>\n",
        "      <th>Insertion average length</th>\n",
        "      <th>Insertion rate per base</th>\n",
        "      <th>Mapping speed, Million of reads per hour</th>\n",
        "      <th>Mismatch rate per base, percent</th>\n",
        "      <th>Number of input reads</th>\n",
        "      <th>Number of reads mapped to multiple loci</th>\n",
        "      <th>Number of reads mapped to too many loci</th>\n",
        "      <th>Number of splices: AT/AC</th>\n",
        "      <th>Number of splices: Annotated (sjdb)</th>\n",
        "      <th>Number of splices: GC/AG</th>\n",
        "      <th>Number of splices: GT/AG</th>\n",
        "      <th>Number of splices: Non-canonical</th>\n",
        "      <th>Number of splices: Total</th>\n",
        "      <th>Started job on</th>\n",
        "      <th>Started mapping on</th>\n",
        "      <th>Uniquely mapped reads %</th>\n",
        "      <th>Uniquely mapped reads number</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>SRR1055094_1.fastq</th>\n",
        "      <td> 0.308652</td>\n",
        "      <td> 0.608815</td>\n",
        "      <td> 5.75%</td>\n",
        "      <td> 0.11%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  7.81%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.84</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:14:39</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1112.30</td>\n",
        "      <td> 0.41%</td>\n",
        "      <td> 31,515,133</td>\n",
        "      <td> 1812852</td>\n",
        "      <td> 35270</td>\n",
        "      <td> 3017</td>\n",
        "      <td> 0</td>\n",
        "      <td> 32622</td>\n",
        "      <td> 4599716</td>\n",
        "      <td> 10731</td>\n",
        "      <td> 4646086</td>\n",
        "      <td> Jan 05 15:09:03</td>\n",
        "      <td> Jan 05 15:12:57</td>\n",
        "      <td> 86.14%</td>\n",
        "      <td> 27,147,902</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055095_1.fastq</th>\n",
        "      <td> 0.344636</td>\n",
        "      <td> 0.633884</td>\n",
        "      <td> 5.63%</td>\n",
        "      <td> 0.11%</td>\n",
        "      <td> 0.19%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  8.40%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.84</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:11:56</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1070.28</td>\n",
        "      <td> 0.41%</td>\n",
        "      <td> 24,973,220</td>\n",
        "      <td> 1405194</td>\n",
        "      <td> 28219</td>\n",
        "      <td> 2526</td>\n",
        "      <td> 0</td>\n",
        "      <td> 25226</td>\n",
        "      <td> 3557819</td>\n",
        "      <td>  8667</td>\n",
        "      <td> 3594238</td>\n",
        "      <td> Jan 05 15:09:05</td>\n",
        "      <td> Jan 05 15:10:32</td>\n",
        "      <td> 85.68%</td>\n",
        "      <td> 21,396,280</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055096_1.fastq</th>\n",
        "      <td> 0.329307</td>\n",
        "      <td> 0.636072</td>\n",
        "      <td> 5.87%</td>\n",
        "      <td> 0.11%</td>\n",
        "      <td> 0.19%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  9.53%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.77</td>\n",
        "      <td> 1.44</td>\n",
        "      <td> 0.01%</td>\n",
        "      <td> Jan 05 15:12:53</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1067.12</td>\n",
        "      <td> 0.45%</td>\n",
        "      <td> 29,642,279</td>\n",
        "      <td> 1739038</td>\n",
        "      <td> 33461</td>\n",
        "      <td> 2850</td>\n",
        "      <td> 0</td>\n",
        "      <td> 28800</td>\n",
        "      <td> 4056540</td>\n",
        "      <td> 10160</td>\n",
        "      <td> 4098350</td>\n",
        "      <td> Jan 05 15:09:07</td>\n",
        "      <td> Jan 05 15:11:13</td>\n",
        "      <td> 84.30%</td>\n",
        "      <td> 24,987,825</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055097_1.fastq</th>\n",
        "      <td> 0.325036</td>\n",
        "      <td> 0.634526</td>\n",
        "      <td> 5.68%</td>\n",
        "      <td> 0.12%</td>\n",
        "      <td> 0.19%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  9.51%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.79</td>\n",
        "      <td> 1.44</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:13:19</td>\n",
        "      <td> 1.31</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1105.39</td>\n",
        "      <td> 0.45%</td>\n",
        "      <td> 33,775,672</td>\n",
        "      <td> 1917575</td>\n",
        "      <td> 41648</td>\n",
        "      <td> 3037</td>\n",
        "      <td> 0</td>\n",
        "      <td> 32323</td>\n",
        "      <td> 4567508</td>\n",
        "      <td> 11389</td>\n",
        "      <td> 4614257</td>\n",
        "      <td> Jan 05 15:09:09</td>\n",
        "      <td> Jan 05 15:11:29</td>\n",
        "      <td> 84.50%</td>\n",
        "      <td> 28,540,433</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055098_1.fastq</th>\n",
        "      <td> 0.277769</td>\n",
        "      <td> 0.599562</td>\n",
        "      <td> 5.64%</td>\n",
        "      <td> 0.13%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  8.08%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.92</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.01%</td>\n",
        "      <td> Jan 05 15:14:17</td>\n",
        "      <td> 1.29</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1179.81</td>\n",
        "      <td> 0.34%</td>\n",
        "      <td> 51,124,989</td>\n",
        "      <td> 2883906</td>\n",
        "      <td> 67631</td>\n",
        "      <td> 4940</td>\n",
        "      <td> 0</td>\n",
        "      <td> 52277</td>\n",
        "      <td> 7246924</td>\n",
        "      <td> 19233</td>\n",
        "      <td> 7323374</td>\n",
        "      <td> Jan 05 15:09:11</td>\n",
        "      <td> Jan 05 15:11:41</td>\n",
        "      <td> 85.96%</td>\n",
        "      <td> 43,948,660</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055099_1.fastq</th>\n",
        "      <td> 0.312152</td>\n",
        "      <td> 0.637419</td>\n",
        "      <td> 5.63%</td>\n",
        "      <td> 0.16%</td>\n",
        "      <td> 0.21%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  9.79%</td>\n",
        "      <td> 100</td>\n",
        "      <td>  98.9</td>\n",
        "      <td> 1.45</td>\n",
        "      <td> 0.01%</td>\n",
        "      <td> Jan 05 15:13:54</td>\n",
        "      <td> 1.31</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1160.21</td>\n",
        "      <td> 0.37%</td>\n",
        "      <td> 42,218,633</td>\n",
        "      <td> 2377636</td>\n",
        "      <td> 66584</td>\n",
        "      <td> 3748</td>\n",
        "      <td> 0</td>\n",
        "      <td> 39629</td>\n",
        "      <td> 5523704</td>\n",
        "      <td> 14615</td>\n",
        "      <td> 5581696</td>\n",
        "      <td> Jan 05 15:09:15</td>\n",
        "      <td> Jan 05 15:11:43</td>\n",
        "      <td> 84.22%</td>\n",
        "      <td> 35,555,761</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055100_1.fastq</th>\n",
        "      <td> 0.321638</td>\n",
        "      <td> 0.617714</td>\n",
        "      <td> 5.67%</td>\n",
        "      <td> 0.13%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  7.85%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.92</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:15:05</td>\n",
        "      <td> 1.27</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1171.31</td>\n",
        "      <td> 0.33%</td>\n",
        "      <td> 34,488,677</td>\n",
        "      <td> 1956562</td>\n",
        "      <td> 45419</td>\n",
        "      <td> 3543</td>\n",
        "      <td> 0</td>\n",
        "      <td> 36040</td>\n",
        "      <td> 5019539</td>\n",
        "      <td> 12873</td>\n",
        "      <td> 5071995</td>\n",
        "      <td> Jan 05 15:12:01</td>\n",
        "      <td> Jan 05 15:13:19</td>\n",
        "      <td> 86.17%</td>\n",
        "      <td> 29,717,200</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055101_1.fastq</th>\n",
        "      <td> 0.402251</td>\n",
        "      <td> 0.665142</td>\n",
        "      <td> 5.62%</td>\n",
        "      <td> 0.13%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  7.79%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.92</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.01%</td>\n",
        "      <td> Jan 05 15:14:49</td>\n",
        "      <td> 1.29</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1142.72</td>\n",
        "      <td> 0.33%</td>\n",
        "      <td> 18,093,056</td>\n",
        "      <td> 1016984</td>\n",
        "      <td> 24233</td>\n",
        "      <td> 1823</td>\n",
        "      <td> 0</td>\n",
        "      <td> 19209</td>\n",
        "      <td> 2672360</td>\n",
        "      <td>  6649</td>\n",
        "      <td> 2700041</td>\n",
        "      <td> Jan 05 15:12:59</td>\n",
        "      <td> Jan 05 15:13:52</td>\n",
        "      <td> 86.28%</td>\n",
        "      <td> 15,610,825</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055102_1.fastq</th>\n",
        "      <td> 0.340816</td>\n",
        "      <td> 0.642169</td>\n",
        "      <td> 5.56%</td>\n",
        "      <td> 0.12%</td>\n",
        "      <td> 0.17%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  8.15%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.94</td>\n",
        "      <td> 1.46</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:15:36</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1184.76</td>\n",
        "      <td> 0.34%</td>\n",
        "      <td> 32,909,921</td>\n",
        "      <td> 1828979</td>\n",
        "      <td> 39251</td>\n",
        "      <td> 3072</td>\n",
        "      <td> 0</td>\n",
        "      <td> 33644</td>\n",
        "      <td> 4689513</td>\n",
        "      <td> 11554</td>\n",
        "      <td> 4737783</td>\n",
        "      <td> Jan 05 15:13:24</td>\n",
        "      <td> Jan 05 15:13:56</td>\n",
        "      <td> 85.99%</td>\n",
        "      <td> 28,300,778</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055103_1.fastq</th>\n",
        "      <td> 0.296351</td>\n",
        "      <td> 0.623671</td>\n",
        "      <td> 5.79%</td>\n",
        "      <td> 0.14%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 10.70%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.84</td>\n",
        "      <td> 1.43</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:16:53</td>\n",
        "      <td> 1.27</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1150.95</td>\n",
        "      <td> 0.42%</td>\n",
        "      <td> 47,636,423</td>\n",
        "      <td> 2757498</td>\n",
        "      <td> 64506</td>\n",
        "      <td> 4347</td>\n",
        "      <td> 0</td>\n",
        "      <td> 44970</td>\n",
        "      <td> 6355442</td>\n",
        "      <td> 16289</td>\n",
        "      <td> 6421048</td>\n",
        "      <td> Jan 05 15:13:40</td>\n",
        "      <td> Jan 05 15:14:24</td>\n",
        "      <td> 83.19%</td>\n",
        "      <td> 39,630,869</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055104_1.fastq</th>\n",
        "      <td> 0.326197</td>\n",
        "      <td> 0.621992</td>\n",
        "      <td> 5.63%</td>\n",
        "      <td> 0.12%</td>\n",
        "      <td> 0.18%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  8.45%</td>\n",
        "      <td> 100</td>\n",
        "      <td>  98.9</td>\n",
        "      <td> 1.45</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> Jan 05 15:16:41</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1147.84</td>\n",
        "      <td> 0.38%</td>\n",
        "      <td> 31,884,368</td>\n",
        "      <td> 1793833</td>\n",
        "      <td> 38676</td>\n",
        "      <td> 3273</td>\n",
        "      <td> 0</td>\n",
        "      <td> 33946</td>\n",
        "      <td> 4710211</td>\n",
        "      <td> 11046</td>\n",
        "      <td> 4758476</td>\n",
        "      <td> Jan 05 15:13:59</td>\n",
        "      <td> Jan 05 15:15:01</td>\n",
        "      <td> 85.62%</td>\n",
        "      <td> 27,300,917</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRR1055105_1.fastq</th>\n",
        "      <td> 0.409478</td>\n",
        "      <td> 0.669906</td>\n",
        "      <td> 5.54%</td>\n",
        "      <td> 0.14%</td>\n",
        "      <td> 0.20%</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td>  8.58%</td>\n",
        "      <td> 100</td>\n",
        "      <td> 98.94</td>\n",
        "      <td> 1.44</td>\n",
        "      <td> 0.01%</td>\n",
        "      <td> Jan 05 15:16:36</td>\n",
        "      <td> 1.30</td>\n",
        "      <td> 0.00%</td>\n",
        "      <td> 1121.41</td>\n",
        "      <td> 0.37%</td>\n",
        "      <td> 18,690,189</td>\n",
        "      <td> 1035997</td>\n",
        "      <td> 26361</td>\n",
        "      <td> 1750</td>\n",
        "      <td> 0</td>\n",
        "      <td> 19119</td>\n",
        "      <td> 2609792</td>\n",
        "      <td>  6400</td>\n",
        "      <td> 2637061</td>\n",
        "      <td> Jan 05 15:14:08</td>\n",
        "      <td> Jan 05 15:15:36</td>\n",
        "      <td> 85.54%</td>\n",
        "      <td> 15,987,401</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>"
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 10,
       "text": [
        "<IPython.core.display.HTML at 0xaa6de10>"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mapper = {\"SRR1055094\" : \"H1_DN\", \n",
      "\"SRR1055095_1.fastq\" : \"H1_KO2\", \n",
      "\"SRR1055096_1.fastq\" : \"H1_AzLo\", \n",
      "\"SRR1055097_1.fastq\" : \"H1_AzHi\", \n",
      "\"SRR1055098_1.fastq\" : \"H2_DN\",\n",
      "\"SRR1055099_1.fastq\" : \"H2_KO2\",\n",
      "\"SRR1055100_1.fastq\" : \"H2_AzLo\",\n",
      "\"SRR1055101_1.fastq\" : \"H2_AzHi\",\n",
      "\"SRR1055102_1.fastq\" : \"H3_DN\",\n",
      "\"SRR1055103_1.fastq\" : \"H3_KO2\",\n",
      "\"SRR1055104_1.fastq\" : \"H3_AzLo\",\n",
      "\"SRR1055105_1.fastq\" : \"H3_AzHi\"}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "datasets = glob.glob(\"/nas3/gpratt/projects/leo/analysis/fucci_rnaseq_v1/*.rpkm\")\n",
      "datasets = {os.path.basename(dataset).split(\"_\")[0] : pd.read_csv(dataset, index_col=0, sep=\"\\t\") for dataset in datasets}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": "*"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "datasets = glob.glob(\"/nas3/gpratt/projects/leo/analysis/fucci_rnaseq_v1/*.rpkm\")\n",
      "datasets = {os.path.basename(dataset).split(\"_\")[0] : pd.read_csv(dataset, index_col=0, sep=\"\\t\") for dataset in datasets}\n",
      "master_df = pd.concat(datasets, join=\"outer\").rename({\"SRR1055094\" : \"H1_DN\", \n",
      "                                                       \"SRR1055095\" : \"H1_KO2\", \n",
      "                                                        \"SRR1055096\" : \"H1_AzLo\", \n",
      "                                                        \"SRR1055097\" : \"H1_AzHi\", \n",
      "                                                        \"SRR1055098\" : \"H2_DN\",\n",
      "                                                        \"SRR1055099\" : \"H2_KO2\",\n",
      "                                                        \"SRR1055100\" : \"H2_AzLo\",\n",
      "                                                        \"SRR1055101\" : \"H2_AzHi\",\n",
      "                                                        \"SRR1055102\" : \"H3_DN\",\n",
      "                                                        \"SRR1055103\" : \"H3_KO2\",\n",
      "                                                        \"SRR1055104\" : \"H3_AzLo\",\n",
      "                                                        \"SRR1055105\" : \"H3_AzHi\"})"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": "*"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "master_df[\"logged_rpkm\"] = master_df.RPKM.apply(log10)\n",
      "logged_rpkm_df = master_df[master_df.logged_rpkm != np.NINF].logged_rpkm\n",
      "def plot_hist2d(name1, name2):\n",
      "    x = logged_rpkm_df.ix[name2]\n",
      "    y = logged_rpkm_df.ix[name1]\n",
      "    x.name = \"one\"\n",
      "    y.name = \"two\"\n",
      "    foo = pd.concat([x, y], axis=1, join=\"inner\")\n",
      "    hist2d(foo.one, foo.two, bins=175, norm=Normalize(), cmin=1, vmin=0, vmax=45)\n",
      "    xlabel(name1, fontsize=18)\n",
      "    ylabel(name2, fontsize=18)\n",
      "    colorbar()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": "*"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "figsize(15,100)\n",
      "ys = len(list(combinations(set(master_df.index.get_level_values(level=0)), 2)))\n",
      "for x, (name1, name2) in enumerate(combinations(set(master_df.index.get_level_values(level=0)), 2)):\n",
      "    subplot((ys / 4) + 1, 4 , x + 1)\n",
      "    #plot_rpkm_vs_rpkm(name1, name2)\n",
      "    plot_hist2d(name1, name2)\n",
      "    title(name2 + \" vs \" + name1 + \" \" + str(scipy.stats.linregress(master_df.ix[name1].RPKM, master_df.ix[name2].RPKM)[2]))\n",
      "    xlim((-4,5))\n",
      "    ylim((-4,5))\n",
      "tight_layout()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": "*"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Need to double check RPKMs, something feels wrong here... "
     ]
    }
   ],
   "metadata": {}
  }
 ]
}