03-Pathway-visualization.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Metabolic pathway maps"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Metabolic pathway visualizations with Escher"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import escher"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Display all available maps in escher"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'map_name': 'e_coli_core.Core metabolism', 'organism': 'Escherichia coli'},\n",
       " {'map_name': 'iJO1366.Central metabolism', 'organism': 'Escherichia coli'},\n",
       " {'map_name': 'iJO1366.Fatty acid beta-oxidation',\n",
       "  'organism': 'Escherichia coli'},\n",
       " {'map_name': 'iJO1366.Fatty acid biosynthesis (saturated)',\n",
       "  'organism': 'Escherichia coli'},\n",
       " {'map_name': 'iJO1366.Nucleotide and histidine biosynthesis',\n",
       "  'organism': 'Escherichia coli'},\n",
       " {'map_name': 'iJO1366.Nucleotide metabolism', 'organism': 'Escherichia coli'},\n",
       " {'map_name': 'RECON1.Amino acid metabolism (partial)',\n",
       "  'organism': 'Homo sapiens'},\n",
       " {'map_name': 'RECON1.Carbohydrate metabolism', 'organism': 'Homo sapiens'},\n",
       " {'map_name': 'RECON1.Glycolysis TCA PPP', 'organism': 'Homo sapiens'},\n",
       " {'map_name': 'RECON1.Inositol retinol metabolism',\n",
       "  'organism': 'Homo sapiens'},\n",
       " {'map_name': 'RECON1.Tryptophan metabolism', 'organism': 'Homo sapiens'},\n",
       " {'map_name': 'iMM904.Central carbon metabolism',\n",
       "  'organism': 'Saccharomyces cerevisiae'}]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "escher.list_available_maps()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Display a map _E. coli_ central carbon metabolism."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
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       "  \n",
       "  \n",
       "    <link rel=\"stylesheet\" href=\"//unpkg.com/escher-vis@1.6.0/css/dist/builder.min.css\"/>\n",
       "  \n",
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       "           var load = function(t_map_data, t_model_data, t_options) {\n",
       "               escher.Builder(t_map_data, t_model_data, data.builder_embed_css,\n",
       "                              escher.libs.d3_select('#' + data.id), t_options);\n",
       "           }\n",
       "\n",
       "           // for the static site, use the url attributes for the map and model\n",
       "           // information\n",
       "           if (data.static_site_index !== null) {\n",
       "               escher.static.load_map_model_from_url(data.map_download_url, data.model_download_url,\n",
       "                                                     data.static_site_index, data.options, load);\n",
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       "               load(data.map_data, data.model_data, data.options);\n",
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       "             paths: {\n",
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       "             },\n",
       "             // Override urlArgs that adds ?v= to the end of the escher URL and\n",
       "             // messes up unpkg links. Honestly, I'm not sure if this will lead\n",
       "             // to downstream bugs in the notebook, but they really shouldn't be\n",
       "             // doing this cache-busting anyway.\n",
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       "<IPython.core.display.HTML object>"
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     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "escher.Builder('e_coli_core.Core metabolism').display_in_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Visualize reaction-centric and/or metabolite-centric data."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
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       "               model_data: JSON.parse('null'),\n",
       "               static_site_index: JSON.parse('null'),\n",
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       "  </script>\n"
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     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "escher.Builder('e_coli_core.Core metabolism',\n",
    "               reaction_data={'PGK': 100},\n",
    "               metabolite_data={'ATP': 20}).display_in_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Exercise (15 min)\n",
    "\n",
    "* Solve the _E. coli_ from the previous session and visualize the computed fluxes on the central carbon metabolism map.\n",
    "* Visualize the same flux distribution on another map (a list of available maps can be retrieved by running `escher.list_available_maps()`)"
   ]
  }
 ],
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