{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "u'/root/jupyter_nbs'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/root\n"
     ]
    }
   ],
   "source": [
    "cd /root"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0m\u001b[01;34mdata\u001b[0m/  \u001b[01;34mjupyter_nbs\u001b[0m/  \u001b[01;34mminiconda2\u001b[0m/  \u001b[01;34mowl_home\u001b[0m/  \u001b[01;34mowl_web\u001b[0m/\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "u'/gitrepos/LabDocs/jupyter_nbs/sam'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/gitrepos/LabDocs\n"
     ]
    }
   ],
   "source": [
    "cd /gitrepos/LabDocs/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CONTRIBUTING.md             OlyO_Master.tsv          labinventory_qrcode.png\r\n",
      "DMPseq.md                   OpenScienceResources.md  \u001b[0m\u001b[01;34mmanuscripts\u001b[0m/\r\n",
      "DataSharePlan.md            PrimerDatabase.tab       \u001b[01;34mnb\u001b[0m/\r\n",
      "GradeScale.txt              Proposal_database.md     pd-position-description.md\r\n",
      "Lab_Inventory.csv           README.md                \u001b[01;34mprotocols\u001b[0m/\r\n",
      "Lab_Software.md             Roberts_SB_Tenure_2.pdf  \u001b[01;34mslidedecks\u001b[0m/\r\n",
      "Next_Gen_Seq_Libraries.tsv  Roberts_cv-Chew.md       \u001b[01;34mtemplates\u001b[0m/\r\n",
      "Nightingales-master.csv     \u001b[01;34mcode\u001b[0m/                    \u001b[01;34mweb\u001b[0m/\r\n",
      "Nightingales.tsv            \u001b[01;34mjupyter_nbs\u001b[0m/\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/gitrepos\n"
     ]
    }
   ],
   "source": [
    "cd .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0m\u001b[01;34m2bRAD_GATK\u001b[0m/  \u001b[01;34mLabDocs\u001b[0m/\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/gitrepos/2bRAD_GATK\n"
     ]
    }
   ],
   "source": [
    "cd 2bRAD_GATK/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2bRAD_GATK_scripts_manual.pdf      \u001b[0m\u001b[01;32mlauncher_creator.py\u001b[0m*\r\n",
      "\u001b[01;32m2bRAD_bowtie2_launch.pl\u001b[0m*           mix_illumina_qpcr.R\r\n",
      "2bRAD_gatk_README.txt              \u001b[01;32mngs_concat.pl\u001b[0m*\r\n",
      "2bRAD_protocol_mar31_2016.pdf      picogreen.R\r\n",
      "\u001b[01;32m2bRAD_trim_launch.pl\u001b[0m*              \u001b[01;32mrecalibrateSNPs_gatk.pl\u001b[0m*\r\n",
      "\u001b[01;32m2bRAD_trim_launch_dedup.pl\u001b[0m*        recalibrate_SNP.tranches.pdf\r\n",
      "2bRAD_trim_launch_dedup2.pl        \u001b[01;32mremoveBayescanOutliers.pl\u001b[0m*\r\n",
      "GetHighQualVcfs.py                 \u001b[01;32mrepMatchStats.pl\u001b[0m*\r\n",
      "README.md                          \u001b[01;32mreplicatesMatch.pl\u001b[0m*\r\n",
      "admixturePlotting.R                \u001b[01;32mretabvcf.pl\u001b[0m*\r\n",
      "\u001b[01;32malleleCounts.pl\u001b[0m*                   \u001b[01;32mrunRepsStructure.pl\u001b[0m*\r\n",
      "analyzeLD.R                        \u001b[01;32mthinner.pl\u001b[0m*\r\n",
      "\u001b[01;32mconcatFasta.pl\u001b[0m*                    \u001b[01;32mtrim2bRAD.pl\u001b[0m*\r\n",
      "dna.mixing.R                       \u001b[01;32mtrim2bRAD_2barcodes.pl\u001b[0m*\r\n",
      "fastStructurePlotting.R            \u001b[01;32mtrim2bRAD_2barcodes_dedup.pl\u001b[0m*\r\n",
      "fastStructurePlotting_functions.R  trim2bRAD_2barcodes_dedup2.pl\r\n",
      "\u001b[01;32mfilterStats_gatk.pl\u001b[0m*               \u001b[01;32mvcf2dadi.pl\u001b[0m*\r\n",
      "genomeScanPlots.R                  \u001b[01;32mvcf2dadi2.pl\u001b[0m*\r\n",
      "\u001b[01;32mhetfilter.pl\u001b[0m*                      \u001b[01;32mvcf2fasta_ref.pl\u001b[0m*\r\n",
      "illumina_mix_data.csv              \u001b[01;32mvcf2map.pl\u001b[0m*\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "ERROR:root:Cell magic `%%R` not found.\n"
     ]
    }
   ],
   "source": [
    "%%R\n",
    "all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "No module named rpy2.ipython",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-691c6d73b073>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'load_ext rpy2.ipython'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2156\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2157\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2158\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2160\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2077\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2078\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2079\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2080\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2081\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-62>\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     35\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mmodule_str\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     36\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mUsageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Missing module name.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextension_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     38\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'already loaded'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc\u001b[0m in \u001b[0;36mload_extension\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     81\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mmodule_str\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     82\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mprepended_to_syspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mipython_extension_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 83\u001b[0;31m                     \u001b[0m__import__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     84\u001b[0m             \u001b[0mmod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     85\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_call_load_ipython_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mImportError\u001b[0m: No module named rpy2.ipython"
     ]
    }
   ],
   "source": [
    "%load_ext rpy2.ipython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "No module named rpy2",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-10-c317c5300f0c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'load_ext rpy2'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2156\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2157\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2158\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2160\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2077\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2078\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2079\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2080\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2081\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-62>\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     35\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mmodule_str\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     36\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mUsageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Missing module name.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextension_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     38\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'already loaded'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc\u001b[0m in \u001b[0;36mload_extension\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     81\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mmodule_str\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     82\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mprepended_to_syspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mipython_extension_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 83\u001b[0;31m                     \u001b[0m__import__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     84\u001b[0m             \u001b[0mmod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     85\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_call_load_ipython_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mImportError\u001b[0m: No module named rpy2"
     ]
    }
   ],
   "source": [
    "%load_ext rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "No module named rpy2.interactive.ipython",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-11-d5ba4dbf60b7>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'load_ext rpy2.interactive.ipython'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2156\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2157\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2158\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2160\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2077\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2078\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2079\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2080\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2081\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-62>\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     35\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mmodule_str\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     36\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mUsageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Missing module name.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextension_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     38\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'already loaded'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc\u001b[0m in \u001b[0;36mload_extension\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     81\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mmodule_str\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     82\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mprepended_to_syspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mipython_extension_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 83\u001b[0;31m                     \u001b[0m__import__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     84\u001b[0m             \u001b[0mmod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     85\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_call_load_ipython_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mImportError\u001b[0m: No module named rpy2.interactive.ipython"
     ]
    }
   ],
   "source": [
    "%load_ext rpy2.interactive.ipython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/root/miniconda2/lib/python2.7/site-packages/IPython/extensions/rmagic.py:11: UserWarning: The rmagic extension in IPython has moved to `rpy2.ipython`, please see `rpy2` documentation.\n",
      "  warnings.warn(\"The rmagic extension in IPython has moved to \"\n"
     ]
    }
   ],
   "source": [
    "%load_ext rmagic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-13-75b8616e5642>, line 1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-13-75b8616e5642>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    pip install rpy2\u001b[0m\n\u001b[0m              ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "pip install rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-14-2da0e9dd9008>, line 1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-14-2da0e9dd9008>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    python pip install rpy2\u001b[0m\n\u001b[0m             ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "python pip install rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/root/miniconda2/bin/pip\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "which pip"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting rpy2\n",
      "  Downloading rpy2-2.8.4.tar.gz (183kB)\n",
      "Requirement already satisfied (use --upgrade to upgrade): six in /root/miniconda2/lib/python2.7/site-packages (from rpy2)\n",
      "Requirement already satisfied (use --upgrade to upgrade): singledispatch in /root/miniconda2/lib/python2.7/site-packages (from rpy2)\n",
      "Building wheels for collected packages: rpy2\n",
      "  Running setup.py bdist_wheel for rpy2: started\n",
      "  Running setup.py bdist_wheel for rpy2: finished with status 'done'\n",
      "  Stored in directory: /root/.cache/pip/wheels/63/61/2e/3f71937be6d9efa37641143e18d76224f62a5128cb6fca926f\n",
      "Successfully built rpy2\n",
      "Installing collected packages: rpy2\n",
      "Successfully installed rpy2-2.8.4\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "You are using pip version 8.1.2, however version 9.0.1 is available.\n",
      "You should consider upgrading via the 'pip install --upgrade pip' command.\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "pip install rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "/root/miniconda2/lib/libreadline.so.6: undefined symbol: PC",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-17-691c6d73b073>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'load_ext rpy2.ipython'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m   2156\u001b[0m         \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2157\u001b[0m         \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2158\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2160\u001b[0m     \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m   2077\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2078\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2079\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2080\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2081\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-62>\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magics/extension.pyc\u001b[0m in \u001b[0;36mload_ext\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     35\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mmodule_str\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     36\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mUsageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Missing module name.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextension_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     38\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'already loaded'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/extensions.pyc\u001b[0m in \u001b[0;36mload_extension\u001b[0;34m(self, module_str)\u001b[0m\n\u001b[1;32m     81\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mmodule_str\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     82\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mprepended_to_syspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mipython_extension_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 83\u001b[0;31m                     \u001b[0m__import__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     84\u001b[0m             \u001b[0mmod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodules\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmodule_str\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     85\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_call_load_ipython_extension\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mrmagic\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mload_ipython_extension\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     50\u001b[0m \u001b[0;31m# numpy and rpy2 imports\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     51\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 52\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mrpy2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrinterface\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mri\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     53\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mrpy2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrobjects\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mro\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     54\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mrpy2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrobjects\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpackages\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mrpacks\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     90\u001b[0m \u001b[0;32mdel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     91\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 92\u001b[0;31m from rpy2.rinterface._rinterface import (baseenv,\n\u001b[0m\u001b[1;32m     93\u001b[0m                                          \u001b[0memptyenv\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     94\u001b[0m                                          \u001b[0mendr\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mImportError\u001b[0m: /root/miniconda2/lib/libreadline.so.6: undefined symbol: PC"
     ]
    }
   ],
   "source": [
    "%load_ext rpy2.ipython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fetching package metadata ...........\n",
      "Solving package specifications: .\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "PackageNotFoundError: Package not found: '' Dependency missing in current linux-64 channels: \n",
      "  - rpy2 -> r 3.3.1*\n",
      "\n",
      "You can search for packages on anaconda.org with\n",
      "\n",
      "    anaconda search -t conda r\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "conda install rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "bash: line 1: syntax error near unexpected token `('\n",
      "bash: line 1: `Rscript all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)'\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "Rscript all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "bash: line 1: syntax error near unexpected token `('\n",
      "bash: line 1: `R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)'\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "R /usr/local/bin/R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/usr/local/bin/R\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "which R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "bash: line 1: syntax error near unexpected token `('\n",
      "bash: line 1: `/usr/local/bin/R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)'\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "/usr/local/bin/R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-23-55bcf82a14a4>, line 1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-23-55bcf82a14a4>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)\u001b[0m\n\u001b[0m            ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading package lists...\n",
      "Building dependency tree...\n",
      "Reading state information...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "E: Unable to locate package rpy2\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "apt-get install rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (<ipython-input-25-57d396b50b13>, line 1)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-25-57d396b50b13>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    conda install -c r rpy2=2.8.2\u001b[0m\n\u001b[0m                ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "conda install -c r rpy2=2.8.2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fetching package metadata .............\n",
      "Solving package specifications: .\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: \n",
      "  - rpy2 2.8.2*\n",
      "\n",
      "You can search for packages on anaconda.org with\n",
      "\n",
      "    anaconda search -t conda rpy2\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "conda install -c r rpy2=2.8.2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fetching package metadata ...........\n",
      "Solving package specifications: .\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "PackageNotFoundError: Package not found: '' Dependency missing in current linux-64 channels: \n",
      "  - rpy2 2.7.8* -> r 3.3.1*\n",
      "\n",
      "You can search for packages on anaconda.org with\n",
      "\n",
      "    anaconda search -t conda r\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "conda install -c bioconda rpy2=2.7.8"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "ERROR:root:Line magic function `%R` not found.\n"
     ]
    }
   ],
   "source": [
    "%R all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "ERROR:root:Line magic function `%install_ext` not found.\n"
     ]
    }
   ],
   "source": [
    "%install_ext rmagic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Run 'anaconda show <USER/PACKAGE>' to get more details:\n",
      "Packages:\n",
      "     Name                      |  Version | Package Types   | Platforms      \n",
      "     ------------------------- |   ------ | --------------- | ---------------\n",
      "     Richarizardd/rpy2         |    2.5.6 | conda           | win-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     andywocky/rpy2            |    2.5.6 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     asmeurer/rpy2             |    2.7.0 | conda           | linux-64, linux-32, osx-64\n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     bce/rpy2                  |          | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     bioconda/rpy2             |    2.7.8 | conda           | linux-64, osx-64\n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     cgat/rpy2                 |    2.6.1 | conda           | linux-64       \n",
      "     cgat/rpy2-lite            |    2.6.1 | conda           | linux-64       \n",
      "     desilinguist/rpy2         |    2.5.4 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     equipoise/rpy2            |    2.3.9 | conda           | win-64         \n",
      "     hisanor/rpy2              |    2.7.9 | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     ijstokes/rpy2             |    2.8.3 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     joshadel/rpy2             |    2.3.9 | conda           | win-64         \n",
      "     jrderuiter/rpy2           |    2.5.3 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     kundajelab/rpy2           |    2.7.0 | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     leriomaggio/rpy2          |    2.4.4 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     omgarcia/rpy2             |    2.8.3 | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     pmlandwehr/rpy2           |    2.8.0 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     r-old/rpy2                |    2.4.2 | conda           | linux-64       \n",
      "     r/rpy2                    |    2.8.2 | conda           | linux-64, win-32, win-64, linux-32, osx-64\n",
      "     ralexx/rpy2               |    2.7.6 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     rdonnelly/rpy2            |          | conda           | linux-64, win-64\n",
      "     rmcgibbo/rpy2             |    2.4.2 | conda           | linux-64       \n",
      "     rmkoesterer/rpy2          |    2.7.4 | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     ryan/rpy2                 |    2.5.6 | conda           | linux-64       \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     sebp/rpy2                 |    2.8.3 | conda           | linux-64, osx-64\n",
      "                                          : Python interface to the R language (embedded R)\n",
      "     trent/rpy2                |    2.3.8 | conda           | linux-64       \n",
      "                                          : http://rpy.sourceforge.net/index.html\n",
      "     xbsd/rpy2                 |    2.4.4 | conda           | osx-64         \n",
      "                                          : Python interface to the R language (embedded R)\n",
      "Found 27 packages\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using Anaconda API: https://api.anaconda.org\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "anaconda search -t conda rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fetching package metadata .............\n",
      "Solving package specifications: ..........\n",
      "\n",
      "Package plan for installation in environment /root/miniconda2:\n",
      "\n",
      "The following packages will be downloaded:\n",
      "\n",
      "    package                    |            build\n",
      "    ---------------------------|-----------------\n",
      "    bzip2-1.0.6                |                3          83 KB\n",
      "    jbig-2.1                   |                0          29 KB\n",
      "    ncurses-5.9                |               10         904 KB\n",
      "    xz-5.2.2                   |                0         644 KB\n",
      "    curl-7.45.0                |                2         684 KB  bioconda\n",
      "    gsl-2.2.1                  |                0         7.7 MB\n",
      "    libtiff-4.0.6              |                2         1.5 MB\n",
      "    pcre-8.39                  |                0         553 KB\n",
      "    conda-4.2.13               |           py27_0         391 KB\n",
      "    harfbuzz-0.9.39            |                1         1.1 MB\n",
      "    pango-1.39.0               |                1         668 KB\n",
      "    r-base-3.3.1               |                5        21.7 MB  r\n",
      "    r-boot-1.3_18              |         r3.3.1_0         578 KB  r\n",
      "    r-cluster-2.0.4            |         r3.3.1_0         470 KB  r\n",
      "    r-codetools-0.2_14         |         r3.3.1_0          45 KB  r\n",
      "    r-foreign-0.8_66           |         r3.3.1_0         220 KB  r\n",
      "    r-kernsmooth-2.23_15       |         r3.3.1_0          84 KB  r\n",
      "    r-lattice-0.20_33          |         r3.3.1_0         699 KB  r\n",
      "    r-mass-7.3_45              |         r3.3.1_0         1.0 MB  r\n",
      "    r-nnet-7.3_12              |         r3.3.1_0          99 KB  r\n",
      "    r-rpart-4.1_10             |         r3.3.1_0         863 KB  r\n",
      "    r-spatial-7.3_11           |         r3.3.1_0         123 KB  r\n",
      "    r-class-7.3_14             |         r3.3.1_0          82 KB  r\n",
      "    r-matrix-1.2_6             |         r3.3.1_0         3.1 MB  r\n",
      "    r-nlme-3.1_128             |         r3.3.1_0         2.0 MB  r\n",
      "    r-mgcv-1.8_12              |         r3.3.1_0         1.9 MB  r\n",
      "    r-survival-2.39_4          |         r3.3.1_0         4.5 MB  r\n",
      "    r-3.3.1                    |         r3.3.1_0          584 B  r\n",
      "    r-recommended-3.3.1        |         r3.3.1_0          758 B  r\n",
      "    rpy2-2.8.1                 |     py27r3.3.1_1         365 KB  r\n",
      "    ------------------------------------------------------------\n",
      "                                           Total:        51.8 MB\n",
      "\n",
      "The following NEW packages will be INSTALLED:\n",
      "\n",
      "    bzip2:         1.0.6-3                    \n",
      "    curl:          7.45.0-2           bioconda\n",
      "    gsl:           2.2.1-0                    \n",
      "    harfbuzz:      0.9.39-1                   \n",
      "    jbig:          2.1-0                      \n",
      "    libtiff:       4.0.6-2                    \n",
      "    ncurses:       5.9-10                     \n",
      "    pango:         1.39.0-1                   \n",
      "    pcre:          8.39-0                     \n",
      "    r:             3.3.1-r3.3.1_0     r       \n",
      "    r-base:        3.3.1-5            r       \n",
      "    r-boot:        1.3_18-r3.3.1_0    r       \n",
      "    r-class:       7.3_14-r3.3.1_0    r       \n",
      "    r-cluster:     2.0.4-r3.3.1_0     r       \n",
      "    r-codetools:   0.2_14-r3.3.1_0    r       \n",
      "    r-foreign:     0.8_66-r3.3.1_0    r       \n",
      "    r-kernsmooth:  2.23_15-r3.3.1_0   r       \n",
      "    r-lattice:     0.20_33-r3.3.1_0   r       \n",
      "    r-mass:        7.3_45-r3.3.1_0    r       \n",
      "    r-matrix:      1.2_6-r3.3.1_0     r       \n",
      "    r-mgcv:        1.8_12-r3.3.1_0    r       \n",
      "    r-nlme:        3.1_128-r3.3.1_0   r       \n",
      "    r-nnet:        7.3_12-r3.3.1_0    r       \n",
      "    r-recommended: 3.3.1-r3.3.1_0     r       \n",
      "    r-rpart:       4.1_10-r3.3.1_0    r       \n",
      "    r-spatial:     7.3_11-r3.3.1_0    r       \n",
      "    r-survival:    2.39_4-r3.3.1_0    r       \n",
      "    rpy2:          2.8.1-py27r3.3.1_1 r       \n",
      "    xz:            5.2.2-0                    \n",
      "\n",
      "The following packages will be UPDATED:\n",
      "\n",
      "    conda:         4.2.12-py27_0               --> 4.2.13-py27_0\n",
      "\n",
      "Proceed ([y]/n)? \n",
      "Fetching packages ...\n",
      "bzip2-1.0.6-3.   0% |                              | ETA:  --:--:--   0.00  B/s\r",
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      "jbig-2.1-0.tar  54% |################               | Time: 0:00:00  15.43 MB/s\r",
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      "ncurses-5.9-10   0% |                              | ETA:  --:--:--   0.00  B/s\r",
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      "xz-5.2.2-0.tar   0% |                              | ETA:  --:--:--   0.00  B/s\r",
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      "curl-7.45.0-2.   0% |                              | ETA:  --:--:--   0.00  B/s\r",
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      "[conda               ]|                                                  |   0%\r",
      "[      COMPLETE      ]|##################################################| 100%\r\n",
      "Linking packages ...\n",
      "[      COMPLETE      ]|                                                  |   0%\r",
      "[bzip2               ]|                                                  |   0%\r",
      "[bzip2               ]|                                                  |   0%\r",
      "[jbig                ]|#                                                 |   3%\r",
      "[ncurses             ]|###                                               |   6%\r",
      "[xz                  ]|#####                                             |  10%\r",
      "[curl                ]|######                                            |  13%\r",
      "[gsl                 ]|########                                          |  16%\r",
      "[libtiff             ]|##########                                        |  20%\r",
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      "[conda               ]|#############                                     |  26%\r",
      "[harfbuzz            ]|###############                                   |  30%\r",
      "[pango               ]|################                                  |  33%\r",
      "[r-base              ]|##################                                |  36%\r",
      "[r-boot              ]|####################                              |  40%\r",
      "[r-cluster           ]|#####################                             |  43%\r",
      "[r-codetools         ]|#######################                           |  46%\r",
      "[r-foreign           ]|#########################                         |  50%\r",
      "[r-kernsmooth        ]|##########################                        |  53%\r",
      "[r-lattice           ]|############################                      |  56%\r",
      "[r-mass              ]|##############################                    |  60%\r",
      "[r-nnet              ]|###############################                   |  63%\r",
      "[r-rpart             ]|#################################                 |  66%\r",
      "[r-spatial           ]|###################################               |  70%\r",
      "[r-class             ]|####################################              |  73%\r",
      "[r-matrix            ]|######################################            |  76%\r",
      "[r-nlme              ]|########################################          |  80%\r",
      "[r-mgcv              ]|#########################################         |  83%\r",
      "[r-survival          ]|###########################################       |  86%\r",
      "[r                   ]|#############################################     |  90%\r",
      "[r-recommended       ]|##############################################    |  93%\r",
      "[rpy2                ]|################################################  |  96%\r",
      "[      COMPLETE      ]|##################################################| 100%\r\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "conda install -c r rpy2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "ERROR:root:Cell magic `%%R` not found.\n"
     ]
    }
   ],
   "source": [
    "%%R\n",
    "all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%load_ext rpy2.ipython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in .External2(C_X11, paste(\"png::\", filename, sep = \"\"), g$width,  : \n",
      "  unable to start device PNG\n",
      "\n",
      "  warnings.warn(x, RRuntimeWarning)\n",
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: In addition: \n",
      "  warnings.warn(x, RRuntimeWarning)\n",
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Warning message:\n",
      "\n",
      "  warnings.warn(x, RRuntimeWarning)\n",
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: In (function (filename = \"Rplot%03d.png\", width = 480, height = 480,  :\n",
      "  warnings.warn(x, RRuntimeWarning)\n",
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: \n",
      " \n",
      "  warnings.warn(x, RRuntimeWarning)\n",
      "/root/miniconda2/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning:  unable to open connection to X11 display ''\n",
      "\n",
      "  warnings.warn(x, RRuntimeWarning)\n"
     ]
    },
    {
     "ename": "RRuntimeError",
     "evalue": "Error in .External2(C_X11, paste(\"png::\", filename, sep = \"\"), g$width,  : \n  unable to start device PNG\n",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRRuntimeError\u001b[0m                             Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-5-8a32374b2bdd>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'R'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mu''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mu'all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m   2113\u001b[0m             \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_expand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2114\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2115\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2116\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2117\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-126>\u001b[0m in \u001b[0;36mR\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc\u001b[0m in \u001b[0;36mR\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n\u001b[1;32m    663\u001b[0m                     \u001b[0mro\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0massign\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlocalconverter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpy2ri\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mval\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    664\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 665\u001b[0;31m         \u001b[0mtmpd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetup_graphics\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    666\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    667\u001b[0m         \u001b[0mtext_output\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc\u001b[0m in \u001b[0;36msetup_graphics\u001b[0;34m(self, args)\u001b[0m\n\u001b[1;32m    413\u001b[0m                 \u001b[0;31m# Note: that %% is to pass into R for interpolation there\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    414\u001b[0m                 ro.r.png(\"%s/Rplots%%03d.png\" % tmpd_fix_slashes,\n\u001b[0;32m--> 415\u001b[0;31m                         **argdict)\n\u001b[0m\u001b[1;32m    416\u001b[0m             \u001b[0;32melif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'svg'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    417\u001b[0m                 self.cairo.CairoSVG(\"%s/Rplot.svg\" % tmpd_fix_slashes,\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    176\u001b[0m                 \u001b[0mv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    177\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mr_k\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 178\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSignatureTranslatedFunction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__call__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    179\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    180\u001b[0m \u001b[0mpattern_link\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mre\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mr'\\\\link\\{(.+?)\\}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    104\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    105\u001b[0m             \u001b[0mnew_kwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconversion\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpy2ri\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 106\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mFunction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__call__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mnew_args\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mnew_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    107\u001b[0m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconversion\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mri2ro\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mres\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    108\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mRRuntimeError\u001b[0m: Error in .External2(C_X11, paste(\"png::\", filename, sep = \"\"), g$width,  : \n  unable to start device PNG\n"
     ]
    }
   ],
   "source": [
    "%%R\n",
    "all_fst <- read.table(\"/root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst\",header = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "UsageError: %%R is a cell magic, but the cell body is empty. Did you mean the line magic %R (single %)?\n"
     ]
    }
   ],
   "source": [
    "%%R Running capabilities();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "RRuntimeError",
     "evalue": "Error in .External2(C_X11, paste(\"png::\", filename, sep = \"\"), g$width,  : \n  unable to start device PNG\n",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRRuntimeError\u001b[0m                             Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-7-32328842bf65>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'R'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mu''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34mu'Running capabilities();'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m   2113\u001b[0m             \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_expand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2114\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2115\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2116\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2117\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<decorator-gen-126>\u001b[0m in \u001b[0;36mR\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/magic.pyc\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    187\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc\u001b[0m in \u001b[0;36mR\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n\u001b[1;32m    663\u001b[0m                     \u001b[0mro\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0massign\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlocalconverter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpy2ri\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mval\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    664\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 665\u001b[0;31m         \u001b[0mtmpd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetup_graphics\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    666\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    667\u001b[0m         \u001b[0mtext_output\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/ipython/rmagic.pyc\u001b[0m in \u001b[0;36msetup_graphics\u001b[0;34m(self, args)\u001b[0m\n\u001b[1;32m    413\u001b[0m                 \u001b[0;31m# Note: that %% is to pass into R for interpolation there\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    414\u001b[0m                 ro.r.png(\"%s/Rplots%%03d.png\" % tmpd_fix_slashes,\n\u001b[0;32m--> 415\u001b[0;31m                         **argdict)\n\u001b[0m\u001b[1;32m    416\u001b[0m             \u001b[0;32melif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'svg'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    417\u001b[0m                 self.cairo.CairoSVG(\"%s/Rplot.svg\" % tmpd_fix_slashes,\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    176\u001b[0m                 \u001b[0mv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    177\u001b[0m                 \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mr_k\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 178\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSignatureTranslatedFunction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__call__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    179\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    180\u001b[0m \u001b[0mpattern_link\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mre\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mr'\\\\link\\{(.+?)\\}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/rpy2/robjects/functions.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    104\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    105\u001b[0m             \u001b[0mnew_kwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconversion\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpy2ri\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 106\u001b[0;31m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mFunction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__call__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mnew_args\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mnew_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    107\u001b[0m         \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconversion\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mri2ro\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mres\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    108\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mRRuntimeError\u001b[0m: Error in .External2(C_X11, paste(\"png::\", filename, sep = \"\"), g$width,  : \n  unable to start device PNG\n"
     ]
    }
   ],
   "source": [
    "%%R\n",
    "Running capabilities();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
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   "language": "python",
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
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