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examples/python/basic/.ipynb_checkpoints/CytoscapeREST_Basic1-checkpoint.ipynb
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examples/python/basic/.ipynb_checkpoints/CytoscapeREST_Basic2-checkpoint.ipynb
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| { | ||
| "metadata": { | ||
| "name": "", | ||
| "signature": "sha256:d6a3efd7903943b5456e9a2eaee13132dae0cec1b7b0edb74c51396fa893f386" | ||
| }, | ||
| "nbformat": 3, | ||
| "nbformat_minor": 0, | ||
| "worksheets": [ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "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", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "\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": {} | ||
| } | ||
| ] | ||
| } |
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