{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## A 3D graph representing the network of coappearances of characters in Victor Hugo's novel Les Miserables ## "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We define our graph as an `igraph.Graph` object. [Python `igraph`](hhttp://igraph.org/python/)\n",
    "is a library for high-performance graph generation  and analysis."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import igraph as ig"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read graph data from a `json` file:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import json\n",
    "\n",
    "data = []\n",
    "with open('miserables.json') as f: \n",
    "    for line in f:\n",
    "        data.append(json.loads(line))        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       "  {u'group': 6, u'name': u'Boulatruelle'},\n",
       "  {u'group': 4, u'name': u'Eponine'},\n",
       "  {u'group': 4, u'name': u'Anzelma'},\n",
       "  {u'group': 5, u'name': u'Woman2'},\n",
       "  {u'group': 0, u'name': u'MotherInnocent'},\n",
       "  {u'group': 0, u'name': u'Gribier'},\n",
       "  {u'group': 7, u'name': u'Jondrette'},\n",
       "  {u'group': 7, u'name': u'Mme.Burgon'},\n",
       "  {u'group': 8, u'name': u'Gavroche'},\n",
       "  {u'group': 5, u'name': u'Gillenormand'},\n",
       "  {u'group': 5, u'name': u'Magnon'},\n",
       "  {u'group': 5, u'name': u'Mlle.Gillenormand'},\n",
       "  {u'group': 5, u'name': u'Mme.Pontmercy'},\n",
       "  {u'group': 5, u'name': u'Mlle.Vaubois'},\n",
       "  {u'group': 5, u'name': u'Lt.Gillenormand'},\n",
       "  {u'group': 8, u'name': u'Marius'},\n",
       "  {u'group': 5, u'name': u'BaronessT'},\n",
       "  {u'group': 8, u'name': u'Mabeuf'},\n",
       "  {u'group': 8, u'name': u'Enjolras'},\n",
       "  {u'group': 8, u'name': u'Combeferre'},\n",
       "  {u'group': 8, u'name': u'Prouvaire'},\n",
       "  {u'group': 8, u'name': u'Feuilly'},\n",
       "  {u'group': 8, u'name': u'Courfeyrac'},\n",
       "  {u'group': 8, u'name': u'Bahorel'},\n",
       "  {u'group': 8, u'name': u'Bossuet'},\n",
       "  {u'group': 8, u'name': u'Joly'},\n",
       "  {u'group': 8, u'name': u'Grantaire'},\n",
       "  {u'group': 9, u'name': u'MotherPlutarch'},\n",
       "  {u'group': 4, u'name': u'Gueulemer'},\n",
       "  {u'group': 4, u'name': u'Babet'},\n",
       "  {u'group': 4, u'name': u'Claquesous'},\n",
       "  {u'group': 4, u'name': u'Montparnasse'},\n",
       "  {u'group': 5, u'name': u'Toussaint'},\n",
       "  {u'group': 10, u'name': u'Child1'},\n",
       "  {u'group': 10, u'name': u'Child2'},\n",
       "  {u'group': 4, u'name': u'Brujon'},\n",
       "  {u'group': 8, u'name': u'Mme.Hucheloup'}]}"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data=data[0]\n",
    "data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[u'nodes', u'links']\n"
     ]
    }
   ],
   "source": [
    "print data.keys()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get the number of nodes:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "77"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "N=len(data['nodes'])\n",
    "N"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define the list of edges:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "L=len(data['links'])\n",
    "Edges=[(data['links'][k]['source'], data['links'][k]['target']) for k in range(L)]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define the Graph object from Edges:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "G=ig.Graph(Edges, directed=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract the node attributes, 'group', and 'name':"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{u'group': 1, u'name': u'Myriel'}"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data['nodes'][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "labels=[]\n",
    "group=[]\n",
    "for node in data['nodes']:\n",
    "    labels.append(node['name'])\n",
    "    group.append(node['group'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get the node positions, set by the Kamada-Kawai layout for 3D graphs:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "layt=G.layout('kk', dim=3) "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`layt` is a list of three elements lists (the coordinates of nodes):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[-2.165298835959627, -3.688710574002034, -1.6020681541017792]"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "layt[5]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set data for the Plotly plot of the graph:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "Xn=[layt[k][0] for k in range(N)]# x-coordinates of nodes\n",
    "Yn=[layt[k][1] for k in range(N)]# y-coordinates\n",
    "Zn=[layt[k][2] for k in range(N)]# z-coordinates\n",
    "Xe=[]\n",
    "Ye=[]\n",
    "Ze=[]\n",
    "for e in Edges:\n",
    "    Xe+=[layt[e[0]][0],layt[e[1]][0], None]# x-coordinates of edge ends\n",
    "    Ye+=[layt[e[0]][1],layt[e[1]][1], None]  \n",
    "    Ze+=[layt[e[0]][2],layt[e[1]][2], None]  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import plotly.plotly as py\n",
    "from plotly.graph_objs import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "trace1=Scatter3d(x=Xe,\n",
    "               y=Ye,\n",
    "               z=Ze,\n",
    "               mode='lines',\n",
    "               line=Line(color='rgb(125,125,125)', width=1),\n",
    "               hoverinfo='none'\n",
    "               )\n",
    "trace2=Scatter3d(x=Xn,\n",
    "               y=Yn,\n",
    "               z=Zn,  \n",
    "               mode='markers',\n",
    "               name='actors',\n",
    "               marker=Marker(symbol='dot',\n",
    "                             size=6, \n",
    "                             color=group, \n",
    "                             colorscale='Viridis',\n",
    "                             line=Line(color='rgb(50,50,50)', width=0.5)\n",
    "                             ),\n",
    "               text=labels,\n",
    "               hoverinfo='text'\n",
    "               )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "\n",
    "axis=dict(showbackground=False,\n",
    "          showline=False,  \n",
    "          zeroline=False,\n",
    "          showgrid=False,\n",
    "          showticklabels=False,\n",
    "          title='' \n",
    "          )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "layout = Layout(\n",
    "         title=\"Network of coappearances of characters in Victor Hugo's novel<br> Les Miserables (3D visualization)\", \n",
    "         width=1000,\n",
    "         height=1000,\n",
    "         showlegend=False,\n",
    "         scene=Scene(  \n",
    "         xaxis=XAxis(axis),\n",
    "         yaxis=YAxis(axis), \n",
    "         zaxis=ZAxis(axis), \n",
    "        ),\n",
    "     margin=Margin(\n",
    "        t=100\n",
    "    ),\n",
    "    hovermode='closest',\n",
    "    annotations=Annotations([\n",
    "           Annotation(\n",
    "           showarrow=False, \n",
    "            text=\"Data source: <a href='http://bost.ocks.org/mike/miserables/miserables.json'>[1]</a>\",\n",
    "            xref='paper',     \n",
    "            yref='paper',     \n",
    "            x=0,  \n",
    "            y=0.1,  \n",
    "            xanchor='left',   \n",
    "            yanchor='bottom',  \n",
    "            font=Font(\n",
    "            size=14 \n",
    "            )     \n",
    "            )\n",
    "        ]),    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "u'https://plot.ly/~empet/9059'"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data=Data([trace1, trace2])\n",
    "py.sign_in('empet', 'jkxft90od0')\n",
    "fig=Figure(data=data, layout=layout)\n",
    "\n",
    "py.plot(fig, filename='Les-Miserables')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<div>\n",
    "    <a href=\"https://plot.ly/~empet/9059/\" target=\"_blank\" title=\"Network of coappearances of characters in Victor Hugo&#39;s novel&lt;br&gt; Les Miserables (3D visualization)\" style=\"display: block; text-align: center;\"><img src=\"https://plot.ly/~empet/9059.png\" alt=\"Network of coappearances of characters in Victor Hugo&#39;s novel&lt;br&gt; Les Miserables (3D visualization)\" style=\"max-width: 100%;width: 1000px;\"  width=\"1000\" onerror=\"this.onerror=null;this.src='https://plot.ly/404.png';\" /></a>\n",
    "    <script data-plotly=\"empet:9059\"  src=\"https://plot.ly/embed.js\" async></script>\n",
    "</div>\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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      "text/html": [
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       "    }*/\n",
       "    div.cell{\n",
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       "        margin-left: 13% !important;\n",
       "        margin-right: auto;\n",
       "    }\n",
       "    #notebook li { /* More space between bullet points */\n",
       "    margin-top:0.8em;\n",
       "    }\n",
       "\n",
       "    h1 {\n",
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       "    }\n",
       "    h2 {\n",
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       "        margin-bottom: 1.5em;\n",
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       "    }\n",
       "    h3 {\n",
       "        font-family: 'Fenix', serif;\n",
       "        %margin-top:12px;\n",
       "        %margin-bottom: 3px;\n",
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       "    .text_cell_render h4 {\n",
       "        font-weight: 300;\n",
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       "        color: rgb(8, 66, 133);\n",
       "        margin-bottom: 0.5em;\n",
       "        margin-top: 0.5em;\n",
       "        display: block;\n",
       "    }\n",
       "    h5 {\n",
       "        font-family: 'Alegreya Sans', sans-serif;\n",
       "    }\n",
       "    .text_cell_render h5 {\n",
       "        font-weight: 300;\n",
       "        font-style: normal;\n",
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       "        margin-bottom: 0em;\n",
       "        margin-top: 1.5em;\n",
       "        display: block;\n",
       "        }\n",
       "    div.text_cell_render{\n",
       "        font-family: 'Alegreya Sans',Computer Modern, \"Helvetica Neue\", Arial, Helvetica, Geneva, sans-serif;\n",
       "        line-height: 145%;\n",
       "        font-size: 130%;\n",
       "        width:900px;\n",
       "        margin-left:auto;\n",
       "        margin-right:auto;\n",
       "        %text-align:justify;\n",
       "        %text-justify:inter-word;\n",
       "    }\n",
       "    \n",
       "    \n",
       "    code{\n",
       "      font-size: 78%;\n",
       "    }\n",
       "    .rendered_html code{\n",
       "        background-color: transparent;\n",
       "        white-space: inherit;   \n",
       "    }\n",
       "    .prompt{\n",
       "        display: None;\n",
       "     }\n",
       "    .rendered_html code{\n",
       "    background-color: transparent;\n",
       "    }\n",
       "\n",
       "    blockquote{\n",
       "      display:block;\n",
       "      background: #f3f3f3;\n",
       "      font-family: \"Open sans\",verdana,arial,sans-serif;\n",
       "      width:610px;\n",
       "      padding: 15px 15px 15px 15px;\n",
       "      text-align:justify;\n",
       "      text-justify:inter-word;\n",
       "      }\n",
       "      blockquote p {\n",
       "        margin-bottom: 0;\n",
       "        line-height: 125%;\n",
       "        font-size: 100%;\n",
       "      }\n",
       "   /* element.style {\n",
       "    } */\n",
       "</style>\n",
       "<script>\n",
       "    MathJax.Hub.Config({\n",
       "                        TeX: {\n",
       "                           extensions: [\"AMSmath.js\"]\n",
       "                           },\n",
       "                tex2jax: {\n",
       "                    inlineMath: [ [\"$\",\"$\"], [\"\\\\(\",\"\\\\)\"] ],\n",
       "                    displayMath: [ [\"$$\",\"$$\"], [\"\\\\[\",\"\\\\]\"] ]\n",
       "                },\n",
       "                displayAlign: \"center\", // Change this to \"center\" to center equations.\n",
       "                \"HTML-CSS\": {\n",
       "                    styles: {\".MathJax_Display\": {\"margin\": 4}}\n",
       "                }\n",
       "        });\n",
       "</script>\n"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from IPython.core.display import HTML\n",
    "def  css_styling():\n",
    "    styles = open(\"./custom.css\", \"r\").read()\n",
    "    return HTML(styles)\n",
    "css_styling()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
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  "language_info": {
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 },
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