Added pathway visualization example notebook.

examples/Pathway Visualizations with Escher.ipynb

@@ -0,0 +1,103 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "from cameo import load_model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "iJO1366 = load_model('iJO1366')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "solution = iJO1366.solve()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "from escher import Builder"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "ename": "ValueError",
+     "evalue": "too many values to unpack",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-10-cc9dea1dbb37>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mpathway\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBuilder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap_name\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'iJO1366.Central metabolism'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreaction_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0mreaction\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mflux\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mreaction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mflux\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msolution\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfluxes\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mabs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m1e-6\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mpathway\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay_in_notebook\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m<ipython-input-10-cc9dea1dbb37>\u001b[0m in \u001b[0;36m<dictcomp>\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mpathway\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBuilder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap_name\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'iJO1366.Central metabolism'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreaction_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0mreaction\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mflux\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mreaction\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mflux\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msolution\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfluxes\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mabs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m1e-6\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mpathway\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay_in_notebook\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mValueError\u001b[0m: too many values to unpack"
+     ]
+    }
+   ],
+   "source": [
+    "pathway = Builder(map_name='iJO1366.Central metabolism', reaction_data={reaction: flux for reaction, flux in solution.fluxes if abs(flux) > 1e-6})\n",
+    "pathway.display_in_notebook()"
+   ]
+  },
+  {
+   "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": "2.7.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}