EncodeReccurentPeaksGCmatched1st2ndDNAshapeDimo.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Results on ENCODE TF ChIP-seq (recurring peaks) using JASPAR2014 binding profiles for ChIP'ed TFs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Data sets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "61 TFs considered here (i.e. associated to a JASPAR profile).\n"
     ]
    }
   ],
   "source": [
    "%config InlineBackend.figure_formats=['svg']\n",
    "%matplotlib inline\n",
    "from matplotlib.pyplot import savefig\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import os\n",
    "from scipy.stats import wilcoxon\n",
    "data = pd.read_csv(\"JASPAR_matrices.txt\", names=[\"JASPAR_id\"])\n",
    "data.index = data.JASPAR_id\n",
    "print \"{0:d} TFs considered here (i.e. associated to a JASPAR profile).\".format(len(data))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def auc_val(inline):\n",
    "    return eval(inline.split(' ')[-1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "rep = '20160125_JasparMatchedMergedChipseqScaledDnashape2ndOrderDimo'\n",
    "for repo in os.listdir(rep):\n",
    "    if repo.startswith('MA0'):\n",
    "        res_file = '{0}/{1}/predictions_results.txt'.format(rep, repo)\n",
    "        if os.path.isfile(res_file):\n",
    "            with open(res_file) as stream:\n",
    "                first_line = stream.readline()\n",
    "                assert first_line.startswith('ROC AUC TFFM+DNAshape')\n",
    "                data.loc[repo, 'TFFM_dnashape_AUROC'] = auc_val(first_line)\n",
    "                second_line = stream.readline()\n",
    "                assert second_line.startswith('PR AUC TFFM+DNAshape')\n",
    "                data.loc[repo, 'TFFM_dnashape_AUPRC'] = auc_val(second_line)\n",
    "                third_line = stream.readline()\n",
    "                assert third_line.startswith('ROC AUC TFFM')\n",
    "                data.loc[repo, 'TFFM_AUROC'] = auc_val(third_line)\n",
    "                fourth_line = stream.readline()\n",
    "                assert fourth_line.startswith('PR AUC TFFM')\n",
    "                data.loc[repo, 'TFFM_AUPRC'] = auc_val(fourth_line)\n",
    "                fifth_line = stream.readline()\n",
    "                assert fifth_line.startswith('ROC AUC PWM+DNAshape')\n",
    "                data.loc[repo, 'PSSM_dnashape_AUROC'] = auc_val(fifth_line)\n",
    "                sixth_line = stream.readline()\n",
    "                assert sixth_line.startswith('PR AUC PWM+DNAshape')\n",
    "                data.loc[repo, 'PSSM_dnashape_AUPRC'] = auc_val(sixth_line)\n",
    "                seventh_line = stream.readline()\n",
    "                assert seventh_line.startswith('ROC AUC PWM')\n",
    "                data.loc[repo, 'PSSM_AUROC'] = auc_val(seventh_line)\n",
    "                eighth_line = stream.readline()\n",
    "                assert eighth_line.startswith('PR AUC PWM')\n",
    "                data.loc[repo, 'PSSM_AUPRC'] = auc_val(eighth_line)\n",
    "                data.loc[repo, 'TFFM_AUROC_improvement'] = (\n",
    "                    data.loc[repo, 'TFFM_dnashape_AUROC'] - data.loc[repo, 'TFFM_AUROC'])\n",
    "                data.loc[repo, 'TFFM_AUPRC_improvement'] = (\n",
    "                    data.loc[repo, 'TFFM_dnashape_AUPRC'] - data.loc[repo, 'TFFM_AUPRC'])\n",
    "                data.loc[repo, 'PSSM_AUROC_improvement'] = (\n",
    "                        data.loc[repo, 'PSSM_dnashape_AUROC'] - data.loc[repo, 'PSSM_AUROC'])\n",
    "                data.loc[repo, 'PSSM_AUPRC_improvement'] = (\n",
    "                            data.loc[repo, 'PSSM_dnashape_AUPRC'] - data.loc[repo, 'PSSM_AUPRC'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "rep = '20160502_JasparMatchedMergedChipseq1merScaledDnashape2ndOrderDimoGradboost'\n",
    "for repo in os.listdir(rep):\n",
    "    if repo.startswith('MA0'):\n",
    "        res_file = '{0}/{1}/predictions_results.txt'.format(rep, repo)\n",
    "        if os.path.isfile(res_file):\n",
    "            with open(res_file) as stream:\n",
    "                first_line = stream.readline()\n",
    "                assert first_line.startswith('ROC AUC 1mer+DNAshape')\n",
    "                data.loc[repo, '4bits_dnashape_AUROC'] = auc_val(first_line)\n",
    "                second_line = stream.readline()\n",
    "                assert second_line.startswith('PR AUC 1mer+DNAshape')\n",
    "                data.loc[repo, '4bits_dnashape_AUPRC'] = auc_val(second_line)\n",
    "                third_line = stream.readline()\n",
    "                assert third_line.startswith('ROC AUC 1mer')\n",
    "                data.loc[repo, '4bits_AUROC'] = auc_val(third_line)\n",
    "                fourth_line = stream.readline()\n",
    "                assert fourth_line.startswith('PR AUC 1mer')\n",
    "                data.loc[repo, '4bits_AUPRC'] = auc_val(fourth_line)\n",
    "                data.loc[repo, '4bits_AUROC_improvement'] = (\n",
    "                    data.loc[repo, '4bits_dnashape_AUROC'] - data.loc[repo, '4bits_AUROC'])\n",
    "                data.loc[repo, '4bits_AUPRC_improvement'] = (\n",
    "                    data.loc[repo, '4bits_dnashape_AUPRC'] - data.loc[repo, '4bits_AUPRC'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## TFFM analyses"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TFFM-based classifiers have higher AUROC in 60 over 61 cases\n",
      "TFFM-based classifiers have higher AUPRC in 58 over 61 cases\n"
     ]
    }
   ],
   "source": [
    "print \"TFFM-based classifiers have higher AUROC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"TFFM_dnashape_AUROC\"] > data[\"TFFM_AUROC\"]]), len(data.dropna()))\n",
    "print \"TFFM-based classifiers have higher AUPRC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"TFFM_dnashape_AUPRC\"] > data[\"TFFM_AUPRC\"]]), len(data.dropna()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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   "source": [
    "mini = min(min(data.dropna()[\"TFFM_AUROC\"]), min(data.dropna()[\"TFFM_dnashape_AUROC\"])) - 0.05\n",
    "maxi = max(max(data.dropna()[\"TFFM_AUROC\"]), max(data.dropna()[\"TFFM_dnashape_AUROC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"TFFM_AUROC\", y=\"TFFM_dnashape_AUROC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUROC (TFFM)\")\n",
    "axes.set_ylabel(\"AUROC (TFFM + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_combinedPeaks_TFFM_TFFM+DNAshape.svg\")\n",
    "\n",
    "mini = min(min(data.dropna()[\"TFFM_AUPRC\"]), min(data.dropna()[\"TFFM_dnashape_AUPRC\"])) - 0.05\n",
    "maxi = max(max(data.dropna()[\"TFFM_AUPRC\"]), max(data.dropna()[\"TFFM_dnashape_AUPRC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"TFFM_AUPRC\", y=\"TFFM_dnashape_AUPRC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUPRC (TFFM)\")\n",
    "axes.set_ylabel(\"AUPRC (TFFM + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_combinedPeaks_TFFM_TFFM+DNAshape.svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WilcoxonResult(statistic=14.0, pvalue=2.2202129399099449e-11)\n",
      "WilcoxonResult(statistic=29.0, pvalue=4.6100602144690691e-11)\n"
     ]
    }
   ],
   "source": [
    "print wilcoxon(data.TFFM_dnashape_AUROC, data.TFFM_AUROC)\n",
    "print wilcoxon(data.TFFM_dnashape_AUPRC, data.TFFM_AUPRC)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "data = data.sort_values(\"TFFM_AUROC_improvement\")\n",
    "axes = data.dropna().plot(y=\"TFFM_AUROC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUROC (TFFM + DNA shape)\\n - AUROC (TFFM)\")\n",
    "axes.set_ylim(min(data.TFFM_AUROC_improvement) - 0.05,\n",
    "              max(data.TFFM_AUROC_improvement) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_combinedPeaks_improvement_TFFM_TFFM+DNAshape.svg\")\n",
    "\n",
    "data = data.sort_values(\"TFFM_AUPRC_improvement\")\n",
    "axes = data.dropna().plot(y=\"TFFM_AUPRC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUPRC (TFFM + DNA shape)\\n - AUPRC (TFFM)\")\n",
    "axes.set_ylim(min(data.TFFM_AUPRC_improvement) - 0.05,\n",
    "              max(data.TFFM_AUPRC_improvement) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_combinedPeaks_improvement_TFFM_TFFM+DNAshape.svg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## PSSM analyses"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PSSM-based classifiers have higher AUROC in 60 over 61 cases\n",
      "PSSM-based classifiers have higher AUPRC in 59 over 61 cases\n"
     ]
    }
   ],
   "source": [
    "print \"PSSM-based classifiers have higher AUROC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"PSSM_dnashape_AUROC\"] > data[\"PSSM_AUROC\"]]), len(data.dropna()))\n",
    "print \"PSSM-based classifiers have higher AUPRC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"PSSM_dnashape_AUPRC\"] > data[\"PSSM_AUPRC\"]]), len(data.dropna()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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   "source": [
    "mini = min(min(data.dropna()[\"PSSM_AUROC\"]), min(data.dropna()[\"PSSM_dnashape_AUROC\"])) - 0.05\n",
    "maxi = max(max(data[\"PSSM_AUROC\"]), max(data[\"PSSM_dnashape_AUROC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"PSSM_AUROC\", y=\"PSSM_dnashape_AUROC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUROC (PSSM)\")\n",
    "axes.set_ylabel(\"AUROC (PSSM + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_PSSM_PSSM+DNAshape.svg\")\n",
    "\n",
    "mini = min(min(data[\"PSSM_AUPRC\"]), min(data[\"PSSM_dnashape_AUPRC\"])) - 0.05\n",
    "maxi = max(max(data[\"PSSM_AUPRC\"]), max(data[\"PSSM_dnashape_AUPRC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"PSSM_AUPRC\", y=\"PSSM_dnashape_AUPRC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUPRC (PSSM)\")\n",
    "axes.set_ylabel(\"AUPRC (PSSM + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_combinedPeaks_PSSM_PSSM+DNAshape.svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WilcoxonResult(statistic=10.0, pvalue=1.8236590464231979e-11)\n",
      "WilcoxonResult(statistic=20.0, pvalue=2.9779146402296801e-11)\n"
     ]
    }
   ],
   "source": [
    "print wilcoxon(data.PSSM_dnashape_AUROC, data.PSSM_AUROC)\n",
    "print wilcoxon(data.PSSM_dnashape_AUPRC, data.PSSM_AUPRC)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "data = data.sort_values(\"PSSM_AUROC_improvement\")\n",
    "axes = data.dropna().plot(y=\"PSSM_AUROC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUROC (PSSM + DNA shape)\\n - AUROC (PSSM)\")\n",
    "axes.set_ylim(min(data.PSSM_AUROC_improvement) - 0.05,\n",
    "              max(data.PSSM_AUROC_improvement) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_combinedPeaks_improvement_PSSM_PSSM+DNAshape.svg\")\n",
    "\n",
    "data = data.sort_values(\"PSSM_AUPRC_improvement\")\n",
    "axes = data.dropna().plot(y=\"PSSM_AUPRC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUPRC (PSSM + DNA shape)\\n - AUPRC (PSSM)\")\n",
    "axes.set_ylim(min(data.PSSM_AUPRC_improvement) - 0.05,\n",
    "              max(data.PSSM_AUPRC_improvement) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_combinedPeaks_improvement_PSSM_PSSM+DNAshape.svg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4-bits analyses"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4bits-based classifiers have higher AUROC in 45 over 61 cases\n",
      "4bits-based classifiers have higher AUPRC in 45 over 61 cases\n"
     ]
    }
   ],
   "source": [
    "print \"4bits-based classifiers have higher AUROC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"4bits_dnashape_AUROC\"] > data[\"4bits_AUROC\"]]), len(data.dropna()))\n",
    "print \"4bits-based classifiers have higher AUPRC in {0:d} over {1:d} cases\".format(\n",
    "    len(data[data[\"4bits_dnashape_AUPRC\"] > data[\"4bits_AUPRC\"]]), len(data.dropna()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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   "source": [
    "mini = min(min(data.dropna()[\"4bits_AUROC\"]), \n",
    "           min(data.dropna()[\"4bits_dnashape_AUROC\"])) - 0.05\n",
    "maxi = max(max(data.dropna()[\"4bits_AUROC\"]), \n",
    "           max(data.dropna()[\"4bits_dnashape_AUROC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"4bits_AUROC\", y=\"4bits_dnashape_AUROC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUROC (4-bits)\")\n",
    "axes.set_ylabel(\"AUROC (4-bits + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_4bits_4bits+DNAshape.svg\")\n",
    "\n",
    "mini = min(min(data.dropna()[\"4bits_AUPRC\"]), \n",
    "           min(data.dropna()[\"4bits_dnashape_AUPRC\"])) - 0.05\n",
    "maxi = max(max(data.dropna()[\"4bits_AUPRC\"]), \n",
    "           max(data.dropna()[\"4bits_dnashape_AUPRC\"])) + 0.05\n",
    "axes = data.dropna().plot(x=\"4bits_AUPRC\", y=\"4bits_dnashape_AUPRC\", kind=\"scatter\")\n",
    "axes.set_xlabel(\"AUPRC (4-bits)\")\n",
    "axes.set_ylabel(\"AUPRC (4-bits + DNA shape)\")\n",
    "axes.plot((mini, maxi), (mini, maxi), 'k--')\n",
    "axes.set_xlim(mini, maxi)\n",
    "axes.set_ylim(mini, maxi)\n",
    "axes.set_aspect('equal')\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_4bits_4bits+DNAshape.svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WilcoxonResult(statistic=501.5, pvalue=0.0014268555520432077)\n",
      "WilcoxonResult(statistic=483.0, pvalue=0.00089363884882705572)\n"
     ]
    }
   ],
   "source": [
    "print wilcoxon(data['4bits_dnashape_AUROC'], data['4bits_AUROC'])\n",
    "print wilcoxon(data['4bits_dnashape_AUPRC'], data['4bits_AUPRC'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
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      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f7eb2034ed0>"
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     "metadata": {},
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   ],
   "source": [
    "data = data.sort_values(\"4bits_AUROC_improvement\")\n",
    "axes = data.dropna().plot(y=\"4bits_AUROC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUROC (4-bits + DNA shape)\\n - AUROC (4-bits)\")\n",
    "axes.set_ylim(min(data['4bits_AUROC_improvement']) - 0.05,\n",
    "              max(data['4bits_AUROC_improvement']) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUROC_improvement_4bits_4bits+DNAshape.svg\")\n",
    "\n",
    "data = data.sort_values(\"4bits_AUPRC_improvement\")\n",
    "axes = data.dropna().plot(y=\"4bits_AUPRC_improvement\", use_index=False, legend=False)\n",
    "axes.tick_params(axis=\"x\", labelbottom='off')\n",
    "axes.set_xlabel(\"{0:d} data sets\".format(len(data.dropna())))\n",
    "axes.set_ylabel(\"AUPRC (4-bits + DNA shape)\\n - AUPRC (4-bits)\")\n",
    "axes.set_ylim(min(data['4bits_AUPRC_improvement']) - 0.05,\n",
    "              max(data['4bits_AUPRC_improvement']) + 0.05)\n",
    "axes.set_aspect(1./axes.get_data_ratio())\n",
    "axes.grid()\n",
    "#savefig(\"AUPRC_improvement_4bits_4bits+DNAshape.svg\")"
   ]
  }
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