networkx experiment

networkx-dna-test.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Populating the interactive namespace from numpy and matplotlib\n"
     ]
    }
   ],
   "source": [
    "%pylab inline\n",
    "import networkx as nx\n",
    "import pandas as pd\n",
    "from skbio import DNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# create a graph with skbio.DNASequence objects as nodes\n",
    "G=nx.Graph()\n",
    "d1 = DNA('AAAAAAAAAA', 'd1')\n",
    "d2 = DNA('CAAAAAAAAA', 'd2')\n",
    "d3 = DNA('TTTTTTTTTT', 'd3')\n",
    "d4 = DNA('TTTTTTTTAA', 'd4')\n",
    "d5 = DNA('TAAAAAAATT', 'd5')\n",
    "G.add_edge(d1, d2)\n",
    "G.add_edge(d3, d4)\n",
    "G.add_edge(d3, d5)\n",
    "G.add_edge(d4, d5)\n",
    "pos=nx.spring_layout(G)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "def get_edge_widths(G, num_bins=3, min_width=1):\n",
    "    result = pd.qcut([u.distance(v) for (u,v) in G.edges()], \n",
    "                     num_bins,\n",
    "                     labels=range(min_width,min_width+num_bins))\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "PMsAAAAASUVORK5CYII=\n"
      ],
      "text/plain": [
       "<matplotlib.figure.Figure at 0x1078c1150>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "nx.draw_networkx_nodes(G, pos, node_size=700)\n",
    "## Question: is passing width a list of floats supported functionality?\n",
    "## Answer: sounds like it - https://github.com/networkx/networkx/issues/1441\n",
    "nx.draw_networkx_edges(G, pos, width=get_edge_widths(G))\n",
    "nx.draw_networkx_labels(G, pos, labels={d:d.id for d in G.nodes()},\n",
    "                        font_size=20, font_family='sans-serif')\n",
    "_ = plt.axis('off')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "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": "2.7.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}