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   "cells": [
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     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "# Basic Workflow 2: NetworkX and Cytoscape\n",
      "\n",
      "\n",
      "by [Keiichiro Ono](http://keiono.github.io/)\n",
      "\n",
      "\n",
      "----\n",
      "\n",
      "![](http://cytoscape.org/images/logo/cy3logoOrange.svg)\n",
      "\n",
      "\n",
      "![](http://ipython.org/_static/IPy_header.png)\n",
      "\n",
      "\n",
      "## Introduction\n",
      "Welcome to the part 2 of basic tutorial.  In this example, you will learn how to use Cytoscape with NetworkX, a very poweful network analysis toolkit.\n",
      "\n",
      "### Prerequisites\n",
      "* Basic knowledge of RESTful API\n",
      "    * [This is a good introduction to REST](http://www.restapitutorial.com/)\n",
      "* Basic Python skill\n",
      "* Basic knowledge of Cytoscape \n",
      "\n",
      "### System Requirments\n",
      "* [Java 7+](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html)\n",
      "* [Cytoscape 3.1.1 or later](http://cytoscape.org/download.html)\n",
      "* Latest version of [cy-rest app](https://github.com/keiono/cy-rest/releases/latest)\n",
      "\n",
      "----\n",
      "## Questions or Feature Requests?\n",
      "Please send them to our [mailing list](https://groups.google.com/forum/#!forum/cytoscape-discuss)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import requests\n",
      "import json\n",
      "import networkx as nx\n",
      "\n",
      "# Basic Setup\n",
      "PORT_NUMBER = 1234\n",
      "BASE = 'http://localhost:' + str(PORT_NUMBER) + '/v1/'\n",
      "\n",
      "# Header for posting data to the server as JSON\n",
      "HEADERS = {'Content-Type': 'application/json'}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Generate Networks with NetworkX\n",
      "\n",
      "### Generate scale-free networks"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "graphs = []\n",
      "\n",
      "# Create 10 small randome networks\n",
      "for i in range(10):\n",
      "    # Generate scale-free graph\n",
      "    g = nx.scale_free_graph(50);\n",
      "    \n",
      "    # Perform simple graph analysis\n",
      "    \n",
      "    # Node statistics\n",
      "    bc = nx.betweenness_centrality(g)\n",
      "    degree = nx.degree(g)\n",
      "    cc = nx.closeness_centrality(g)\n",
      "    nx.set_node_attributes(g, 'betweenness', bc)\n",
      "    nx.set_node_attributes(g, 'closeness', cc)\n",
      "    nx.set_node_attributes(g, 'degree', degree)\n",
      "    \n",
      "    # Network statistics\n",
      "    g.graph[\"avg_shortest_path_len\"] = nx.average_shortest_path_length(g)\n",
      "    g.graph[\"density\"] = nx.density(g)\n",
      "    graphs.append(g)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### Send all network models to Cytoscape"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Remove all networks\n",
      "requests.delete(BASE + 'networks')\n",
      "\n",
      "import cytoscape.viewer as cy\n",
      "\n",
      "for graph in graphs:\n",
      "    cyjs_network = cy.from_networkx(graph)\n",
      "    res1 = requests.post(BASE + 'networks', data=json.dumps(cyjs_network), headers=HEADERS)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## (Now graphs are in Cytoscape.  Do analysis, visualization, etc...)"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Get the visualization back to this notebook."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "response = requests.get(BASE + 'networks?format=SUID')\n",
      "network_list = json.loads(response.content)\n",
      "print(network_list)\n",
      "\n",
      "network_views = []\n",
      "for suid in network_list:\n",
      "    response2 = requests.get(BASE + 'networks/' + str(suid) + \"/views/first\")\n",
      "    network_views.append(json.loads(response2.content))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[64700, 66370, 66720, 64008, 66054, 64362, 65726, 65028, 67068, 65340]\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Visual Style can be a simple Python object!\n",
      "\n",
      "my_style = {\n",
      "  \"title\" : \"My Style 10\",\n",
      "  \"defaults\" : [ {\n",
      "    \"visualProperty\" : \"EDGE_WIDTH\",\n",
      "    \"value\" : 11.0\n",
      "  }, {\n",
      "    \"visualProperty\" : \"EDGE_STROKE_UNSELECTED_PAINT\",\n",
      "    \"value\" : \"#00ddff\"\n",
      "  }, {\n",
      "    \"visualProperty\" : \"NODE_WIDTH\",\n",
      "    \"value\" : 20\n",
      "  }, {\n",
      "    \"visualProperty\" : \"NODE_HEIGHT\",\n",
      "    \"value\" : 20\n",
      "  }],\n",
      "  \"mappings\" : [ {\n",
      "    \"mappingType\" : \"discrete\",\n",
      "    \"mappingColumn\" : \"degree\",\n",
      "    \"mappingColumnType\" : \"Integer\",\n",
      "    \"visualProperty\" : \"NODE_FILL_COLOR\",\n",
      "    \"map\" : [ {\n",
      "      \"key\" : \"1\",\n",
      "      \"value\" : \"#440055\"\n",
      "    }, {\n",
      "      \"key\" : \"4\",\n",
      "      \"value\" : \"#00FF11\"\n",
      "    } ]\n",
      "  }, {\n",
      "    \"mappingType\" : \"passthrough\",\n",
      "    \"mappingColumn\" : \"name\",\n",
      "    \"mappingColumnType\" : \"String\",\n",
      "    \"visualProperty\" : \"NODE_LABEL\"\n",
      "  } ]\n",
      "}\n",
      "\n",
      "requests.post(BASE + \"styles\", data=json.dumps(my_style), headers=HEADERS)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 11,
       "text": [
        "<Response [200]>"
       ]
      }
     ],
     "prompt_number": 11
    }
   ],
   "metadata": {}
  }
 ]
}