{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "if (window['cytoscape'] === undefined) {\n",
       "    var paths = {\n",
       "        cytoscape: 'http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min'\n",
       "    };\n",
       "\n",
       "    require.config({\n",
       "        paths: paths\n",
       "    });\n",
       "\n",
       "    require(['cytoscape'], function (cytoscape) {\n",
       "        console.log('Loading Cytoscape.js Module...');\n",
       "        window['cytoscape'] = cytoscape;\n",
       "\n",
       "        var event = document.createEvent(\"HTMLEvents\");\n",
       "        event.initEvent(\"load_cytoscape\", true, false);\n",
       "        window.dispatchEvent(event);\n",
       "    });\n",
       "}"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "ename": "ImportError",
     "evalue": "No module named rpy2.robjects.packages",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-ed5dda1dbc56>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0migraph\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mig\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \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[0mrpackages\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m: No module named rpy2.robjects.packages"
     ]
    }
   ],
   "source": [
    "from py2cytoscape.data.cynetwork import CyNetwork\n",
    "from py2cytoscape.data.cyrest_client import CyRestClient\n",
    "from py2cytoscape.data.style import StyleUtil\n",
    "import py2cytoscape.util.cytoscapejs as cyjs\n",
    "import py2cytoscape.cytoscapejs as renderer\n",
    "\n",
    "import networkx as nx\n",
    "import pandas as pd\n",
    "import json\n",
    "\n",
    "import igraph as ig\n",
    "\n",
    "import rpy2.robjects.packages as rpackages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 117,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<py2cytoscape.data.cynetwork.CyNetwork at 0x10b80dd50>"
      ]
     },
     "execution_count": 117,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "NUM_NODES = 100\n",
    "\n",
    "g1 = ig.Graph.Barabasi(NUM_NODES, 2)\n",
    "g2 = ig.Graph.GRG(NUM_NODES, 0.2)\n",
    "\n",
    "cy = CyRestClient()\n",
    "cy.network.create_from_igraph(g1)\n",
    "cy.network.create_from_igraph(g2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 148,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,27,{'y': 0.4122450976155393, 'x': 0.26689583205779077, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,37,{'y': 0.4413342902926116, 'x': 0.4042221456555569, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,42,{'y': 0.3919489906377719, 'x': 0.4447844056662684, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,43,{'y': 0.4770437889078536, 'x': 0.4455614569474644, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,44,{'y': 0.7063847186804972, 'x': 0.4719754150531076, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,46,{'y': 0.4894698809295054, 'x': 0.48049028523140314, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,48,{'y': 0.4316934429074447, 'x': 0.48068638848412193, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,54,{'y': 0.5463835210708057, 'x': 0.5826852935480062, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,55,{'y': 0.4600141507637713, 'x': 0.5841189250955006, 'label': -1, 'community': 1, 'f1': None})]\n",
      "27\n",
      "37\n",
      "42\n",
      "43\n",
      "44\n",
      "46\n",
      "48\n",
      "54\n",
      "55\n",
      "39\n",
      "47\n",
      "50\n",
      "59\n",
      "64\n",
      "67\n",
      "69\n"
     ]
    }
   ],
   "source": [
    "g2.vs['label'] = [-1]*NUM_NODES\n",
    "fix = [False]*NUM_NODES\n",
    "\n",
    "\n",
    "node0 = g2.vs[40]\n",
    "node1 = g2.vs[57]\n",
    "\n",
    "\n",
    "ne1= node0.neighbors()\n",
    "ne2= node1.neighbors()\n",
    "\n",
    "print(ne1)\n",
    "\n",
    "\n",
    "g2.vs[40]['label'] = 1 \n",
    "g2.vs[57]['label'] = 1 \n",
    "\n",
    "for n in ne1:\n",
    "    print(n.index)\n",
    "    g2.vs[n.index]['label'] = 1\n",
    "    \n",
    "for n in ne2:\n",
    "    print(n.index)\n",
    "    g2.vs[n.index]['label'] = 1\n",
    "\n",
    "fix[40] = True\n",
    "fix[57] = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 149,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<py2cytoscape.data.cynetwork.CyNetwork at 0x10b981410>"
      ]
     },
     "execution_count": 149,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "res = g2.community_label_propagation(initial='label')\n",
    "\n",
    "g2.vs['community'] = res.membership\n",
    "\n",
    "cy.network.create_from_igraph(g2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 167,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "yhq = pd.read_csv('/Applications/Cytoscape_v3.2.1/sampleData/yeastHighQuality.sif', sep=' ', names=['s', 'itr', 't'])\n",
    "yhq = yhq.drop('itr', 1)\n",
    "yhq.head()\n",
    "\n",
    "yhq.to_csv('yhq.el', sep=' ')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 168,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "InternalError",
     "evalue": "Error at foreign.c:101: parsing edgelist file failed, Parse error",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mInternalError\u001b[0m                             Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-168-127fd4c64011>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGraph\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mRead_Edgelist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'yhq.el'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mInternalError\u001b[0m: Error at foreign.c:101: parsing edgelist file failed, Parse error"
     ]
    }
   ],
   "source": [
    "ig.Graph.Read_Edgelist('yhq.el')"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}