prototypes/Read in XML graph data with NetworkX.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\dev\\apps\\Anaconda3\\lib\\site-packages\\networkx\\drawing\\nx_pylab.py:126: MatplotlibDeprecationWarning:\n",
      "\n",
      "pyplot.hold is deprecated.\n",
      "    Future behavior will be consistent with the long-time default:\n",
      "    plot commands add elements without first clearing the\n",
      "    Axes and/or Figure.\n",
      "\n",
      "C:\\dev\\apps\\Anaconda3\\lib\\site-packages\\networkx\\drawing\\nx_pylab.py:138: MatplotlibDeprecationWarning:\n",
      "\n",
      "pyplot.hold is deprecated.\n",
      "    Future behavior will be consistent with the long-time default:\n",
      "    plot commands add elements without first clearing the\n",
      "    Axes and/or Figure.\n",
      "\n",
      "C:\\dev\\apps\\Anaconda3\\lib\\site-packages\\matplotlib\\__init__.py:917: UserWarning:\n",
      "\n",
      "axes.hold is deprecated. Please remove it from your matplotlibrc and/or style files.\n",
      "\n",
      "C:\\dev\\apps\\Anaconda3\\lib\\site-packages\\matplotlib\\rcsetup.py:152: UserWarning:\n",
      "\n",
      "axes.hold is deprecated, will be removed in 3.0\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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muk4Le6OmxvXzAAC0IrxWsOXlUo8eP72ZyVMXXyyVlXF3MQCgReG1gs3L8/0Y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\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x2ba7926d9b0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import networkx as nx\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "G = nx.read_graphml('datasets/test.graphml')\n",
    "nx.draw(G)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "plot() missing 1 required positional argument: 'figure_or_data'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-15-f61c6d700aff>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mplotly\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 6\u001b[1;33m \u001b[0mplotly\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0moffline\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      7\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      8\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mnetworkx\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mnx\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mTypeError\u001b[0m: plot() missing 1 required positional argument: 'figure_or_data'"
     ]
    }
   ],
   "source": [
    "import plotly.plotly as py\n",
    "from plotly.graph_objs import *\n",
    "\n",
    "import plotly\n",
    "plotly.offline.plot()bb\n",
    "\n",
    "import networkx as nx\n",
    "\n",
    "G=nx.random_geometric_graph(200,0.125)\n",
    "pos=nx.get_node_attributes(G,'pos')\n",
    "\n",
    "dmin=1\n",
    "ncenter=0\n",
    "for n in pos:\n",
    "    x,y=pos[n]\n",
    "    d=(x-0.5)**2+(y-0.5)**2\n",
    "    if d<dmin:\n",
    "        ncenter=n\n",
    "        dmin=d\n",
    "\n",
    "p=nx.single_source_shortest_path_length(G,ncenter)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "edge_trace = Scatter(\n",
    "    x=[],\n",
    "    y=[],\n",
    "    line=Line(width=0.5,color='#888'),\n",
    "    hoverinfo='none',\n",
    "    mode='lines')\n",
    "\n",
    "for edge in G.edges():\n",
    "    x0, y0 = G.node[edge[0]]['pos']\n",
    "    x1, y1 = G.node[edge[1]]['pos']\n",
    "    edge_trace['x'] += [x0, x1, None]\n",
    "    edge_trace['y'] += [y0, y1, None]\n",
    "\n",
    "node_trace = Scatter(\n",
    "    x=[],\n",
    "    y=[],\n",
    "    text=[],\n",
    "    mode='markers',\n",
    "    hoverinfo='text',\n",
    "    marker=Marker(\n",
    "        showscale=True,\n",
    "        # colorscale options\n",
    "        # 'Greys' | 'Greens' | 'Bluered' | 'Hot' | 'Picnic' | 'Portland' |\n",
    "        # Jet' | 'RdBu' | 'Blackbody' | 'Earth' | 'Electric' | 'YIOrRd' | 'YIGnBu'\n",
    "        colorscale='YIGnBu',\n",
    "        reversescale=True,\n",
    "        color=[],\n",
    "        size=10,\n",
    "        colorbar=dict(\n",
    "            thickness=15,\n",
    "            title='Node Connections',\n",
    "            xanchor='left',\n",
    "            titleside='right'\n",
    "        ),\n",
    "        line=dict(width=2)))\n",
    "\n",
    "for node in G.nodes():\n",
    "    x, y = G.node[node]['pos']\n",
    "    node_trace['x'].append(x)\n",
    "    node_trace['y'].append(y)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "for node, adjacencies in enumerate(G.adjacency_list()):\n",
    "    node_trace['marker']['color'].append(len(adjacencies))\n",
    "    node_info = '# of connections: '+str(len(adjacencies))\n",
    "    node_trace['text'].append(node_info)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = Figure(data=Data([edge_trace, node_trace]),\n",
    "             layout=Layout(\n",
    "                title='<br>Network graph made with Python',\n",
    "                titlefont=dict(size=16),\n",
    "                showlegend=False,\n",
    "                hovermode='closest',\n",
    "                margin=dict(b=20,l=5,r=5,t=40),\n",
    "                annotations=[ dict(\n",
    "                    text=\"Python code: <a href='https://plot.ly/ipython-notebooks/network-graphs/'> https://plot.ly/ipython-notebooks/network-graphs/</a>\",\n",
    "                    showarrow=False,\n",
    "                    xref=\"paper\", yref=\"paper\",\n",
    "                    x=0.005, y=-0.002 ) ],\n",
    "                xaxis=XAxis(showgrid=False, zeroline=False, showticklabels=False),\n",
    "                yaxis=YAxis(showgrid=False, zeroline=False, showticklabels=False)))\n",
    "\n",
    "py.iplot(fig, filename='networkx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "'module' object is not callable",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-18-769dbdacec9a>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mplotly\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mplotly\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mpy\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      2\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mplotly\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 3\u001b[1;33m \u001b[0mplotly\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0moffline\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      4\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[0mplotly\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mgraph_objs\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[1;33m*\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mTypeError\u001b[0m: 'module' object is not callable"
     ]
    }
   ],
   "source": [
    "import plotly.plotly as py\n",
    "import plotly\n",
    "plotly.offline()\n",
    "from plotly.graph_objs import *\n",
    "\n",
    "trace0 = Scatter(\n",
    "    x=[1, 2, 3, 4],\n",
    "    y=[10, 15, 13, 17]\n",
    ")\n",
    "trace1 = Scatter(\n",
    "    x=[1, 2, 3, 4],\n",
    "    y=[16, 5, 11, 9]\n",
    ")\n",
    "data = Data([trace0, trace1])\n",
    "\n",
    "py.plot(data, filename = 'basic-line')"
   ]
  }
 ],
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