{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualizing time series metabolome profile\n",
    "\n",
    "by Kozo Nishida (Riken, Japan)\n",
    "\n",
    "\n",
    "## Software Requirments\n",
    "\n",
    "Please install the following software packages to run this workflow:\n",
    "\n",
    "* [KEGGscape](http://apps.cytoscape.org/apps/keggscape)\n",
    "* [enhancedGraphics](http://apps.cytoscape.org/apps/enhancedgraphics)\n",
    "\n",
    "\n",
    "### Background\n",
    "This is a sample workflow to automate complex Cytoscape data integaration/visualization process.  Please read the following document for more background:  \n",
    "\n",
    "* https://github.com/idekerlab/KEGGscape/wiki/How-to-visualize-time-series-metabolome-profile\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import json\n",
    "import requests\n",
    "import pandas as pd\n",
    "\n",
    "PORT_NUMBER = 1234\n",
    "BASE_URL = \"http://localhost:\" + str(PORT_NUMBER) + \"/v1/\"\n",
    "HEADERS = {'Content-Type': 'application/json'}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load a KGML pathway data file from KEGG REST API"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Pathway SUID = 71718\n"
     ]
    }
   ],
   "source": [
    "pathway_location = \"http://rest.kegg.jp/get/ath00020/kgml\"\n",
    "res1 = requests.post(BASE_URL + \"networks?source=url\", data=json.dumps([pathway_location]), headers=HEADERS)\n",
    "result = json.loads(res1.content)\n",
    "pathway_suid = result[0][\"networkSUID\"][0]\n",
    "\n",
    "print(\"Pathway SUID = \" + str(pathway_suid))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load table data file as Pandas DataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Metabolite</th>\n",
       "      <th>KEGG</th>\n",
       "      <th>ld20t14</th>\n",
       "      <th>ld20t16</th>\n",
       "      <th>ld20t20</th>\n",
       "      <th>ld20t24</th>\n",
       "      <th>ld20t28</th>\n",
       "      <th>ld20t32</th>\n",
       "      <th>ld20t36</th>\n",
       "      <th>ld20t40</th>\n",
       "      <th>ld20t44</th>\n",
       "      <th>ld20t48</th>\n",
       "      <th>ld20t52</th>\n",
       "      <th>ld20t56</th>\n",
       "      <th>ld20t60</th>\n",
       "      <th>ld20t64</th>\n",
       "      <th>ld20t68</th>\n",
       "      <th>ld20t72</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Alanine</td>\n",
       "      <td>C00041</td>\n",
       "      <td>-0.051007</td>\n",
       "      <td>0.040631</td>\n",
       "      <td>-0.165335</td>\n",
       "      <td>-0.126382</td>\n",
       "      <td>-0.093879</td>\n",
       "      <td>-0.102625</td>\n",
       "      <td>0.009509</td>\n",
       "      <td>0.051824</td>\n",
       "      <td>-0.137530</td>\n",
       "      <td>-0.140400</td>\n",
       "      <td>-0.116827</td>\n",
       "      <td>-0.060302</td>\n",
       "      <td>0.027001</td>\n",
       "      <td>0.081365</td>\n",
       "      <td>-0.060153</td>\n",
       "      <td>-0.097988</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Valine</td>\n",
       "      <td>C00183</td>\n",
       "      <td>-0.025403</td>\n",
       "      <td>-0.003585</td>\n",
       "      <td>-0.058986</td>\n",
       "      <td>-0.069280</td>\n",
       "      <td>-0.129784</td>\n",
       "      <td>-0.092210</td>\n",
       "      <td>0.009129</td>\n",
       "      <td>-0.068003</td>\n",
       "      <td>-0.105905</td>\n",
       "      <td>-0.097984</td>\n",
       "      <td>-0.095181</td>\n",
       "      <td>-0.021911</td>\n",
       "      <td>-0.021224</td>\n",
       "      <td>-0.028314</td>\n",
       "      <td>-0.032834</td>\n",
       "      <td>-0.025435</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Leucine</td>\n",
       "      <td>C00123</td>\n",
       "      <td>-0.005918</td>\n",
       "      <td>0.058287</td>\n",
       "      <td>-0.049900</td>\n",
       "      <td>-0.075853</td>\n",
       "      <td>-0.098339</td>\n",
       "      <td>-0.003847</td>\n",
       "      <td>0.056037</td>\n",
       "      <td>-0.104399</td>\n",
       "      <td>-0.122298</td>\n",
       "      <td>-0.098051</td>\n",
       "      <td>-0.082529</td>\n",
       "      <td>0.027760</td>\n",
       "      <td>-0.006289</td>\n",
       "      <td>-0.048610</td>\n",
       "      <td>-0.042620</td>\n",
       "      <td>-0.000897</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Isoleucine</td>\n",
       "      <td>C00407</td>\n",
       "      <td>0.079870</td>\n",
       "      <td>0.101324</td>\n",
       "      <td>-0.103993</td>\n",
       "      <td>-0.041534</td>\n",
       "      <td>-0.020148</td>\n",
       "      <td>0.066486</td>\n",
       "      <td>0.091006</td>\n",
       "      <td>-0.027547</td>\n",
       "      <td>-0.193494</td>\n",
       "      <td>-0.144676</td>\n",
       "      <td>-0.015375</td>\n",
       "      <td>0.070540</td>\n",
       "      <td>0.118164</td>\n",
       "      <td>0.013795</td>\n",
       "      <td>-0.060418</td>\n",
       "      <td>-0.042314</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Glycine</td>\n",
       "      <td>C00037</td>\n",
       "      <td>-0.056155</td>\n",
       "      <td>-0.185757</td>\n",
       "      <td>-0.857195</td>\n",
       "      <td>-0.725952</td>\n",
       "      <td>-0.051028</td>\n",
       "      <td>0.069038</td>\n",
       "      <td>0.042867</td>\n",
       "      <td>0.098185</td>\n",
       "      <td>-0.445921</td>\n",
       "      <td>-0.893788</td>\n",
       "      <td>-0.201299</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.064322</td>\n",
       "      <td>-0.090597</td>\n",
       "      <td>-0.637518</td>\n",
       "      <td>-0.874438</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metabolite    KEGG   ld20t14   ld20t16   ld20t20   ld20t24   ld20t28  \\\n",
       "0     Alanine  C00041 -0.051007  0.040631 -0.165335 -0.126382 -0.093879   \n",
       "1      Valine  C00183 -0.025403 -0.003585 -0.058986 -0.069280 -0.129784   \n",
       "2     Leucine  C00123 -0.005918  0.058287 -0.049900 -0.075853 -0.098339   \n",
       "3  Isoleucine  C00407  0.079870  0.101324 -0.103993 -0.041534 -0.020148   \n",
       "4     Glycine  C00037 -0.056155 -0.185757 -0.857195 -0.725952 -0.051028   \n",
       "\n",
       "    ld20t32   ld20t36   ld20t40   ld20t44   ld20t48   ld20t52   ld20t56  \\\n",
       "0 -0.102625  0.009509  0.051824 -0.137530 -0.140400 -0.116827 -0.060302   \n",
       "1 -0.092210  0.009129 -0.068003 -0.105905 -0.097984 -0.095181 -0.021911   \n",
       "2 -0.003847  0.056037 -0.104399 -0.122298 -0.098051 -0.082529  0.027760   \n",
       "3  0.066486  0.091006 -0.027547 -0.193494 -0.144676 -0.015375  0.070540   \n",
       "4  0.069038  0.042867  0.098185 -0.445921 -0.893788 -0.201299  0.000000   \n",
       "\n",
       "    ld20t60   ld20t64   ld20t68   ld20t72  \n",
       "0  0.027001  0.081365 -0.060153 -0.097988  \n",
       "1 -0.021224 -0.028314 -0.032834 -0.025435  \n",
       "2 -0.006289 -0.048610 -0.042620 -0.000897  \n",
       "3  0.118164  0.013795 -0.060418 -0.042314  \n",
       "4 -0.064322 -0.090597 -0.637518 -0.874438  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "profile_csv = \"https://raw.githubusercontent.com/idekerlab/KEGGscape/develop/wiki/data/light-dark-20.csv\"\n",
    "profile_df = pd.read_csv(profile_csv)\n",
    "profile_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Convert the DataFrame to JSON and send it to Cytoscape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "profile = json.loads(profile_df.to_json(orient=\"records\"))\n",
    "# print(json.dumps(profile, indent=4))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Response [200]>"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_table_data = {\n",
    "    \"key\": \"KEGG_NODE_LABEL\",\n",
    "    \"dataKey\": \"KEGG\",\n",
    "    \"data\": profile\n",
    "}\n",
    "\n",
    "update_table_url =  BASE_URL + \"networks/\" + str(pathway_suid) + \"/tables/defaultnode\"\n",
    "requests.put(update_table_url, data=json.dumps(new_table_data), headers=HEADERS)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Set values to the chart column"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Response [200]>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chart_entry = 'barchart: attributelist=\"ld20t14,ld20t16,ld20t20,ld20t24,ld20t28,ld20t32,ld20t36,ld20t40,ld20t44,ld20t48,ld20t52,ld20t56,ld20t60,ld20t64,ld20t68,ld20t72\" colorlist=\"up:red,zero:red,down:red\" showlabels=\"false\"'\n",
    "\n",
    "target_row_url = BASE_URL + \"networks/\" + str(pathway_suid) + \"/tables/defaultnode/columns/KEGG\"\n",
    "res2 = requests.get(target_row_url)\n",
    "matched = json.loads(res2.content)[\"values\"]\n",
    "\n",
    "df2 = pd.DataFrame(columns=[\"id\", \"chart\"]);\n",
    "df2[\"id\"] = matched\n",
    "df2[\"chart\"] = chart_entry\n",
    "\n",
    "data = json.loads(df2.to_json(orient=\"records\"))\n",
    "    \n",
    "chart_data = {\n",
    "    \"key\": \"KEGG\",\n",
    "    \"dataKey\": \"id\",\n",
    "    \"data\": data\n",
    "}\n",
    "\n",
    "requests.put(update_table_url, data=json.dumps(chart_data), headers=HEADERS)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Create Visual Style for Custom Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Response [201]>"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "custom_graphics_mapping = {\n",
    "    \"mappingType\" : \"passthrough\",\n",
    "    \"mappingColumn\" : \"chart\",\n",
    "    \"mappingColumnType\" : \"String\",\n",
    "    \"visualProperty\" : \"NODE_CUSTOMGRAPHICS_1\"\n",
    "}\n",
    "\n",
    "style_url = BASE_URL + \"styles/KEGG Style/mappings\"\n",
    "requests.post(style_url, data=json.dumps([custom_graphics_mapping]), headers=HEADERS)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Uncheck the **Fit Custom Graphics to node** box, and bundle edges from menubar.\n",
    "![](https://raw.githubusercontent.com/idekerlab/cy-rest-python/develop/advanced/uncheck-checkbox.png)\n",
    "![](https://raw.githubusercontent.com/idekerlab/cy-rest-python/develop/advanced/bundle-edges.png)\n",
    "\n",
    "You will see\n",
    "![](https://raw.githubusercontent.com/idekerlab/cy-rest-python/develop/advanced/metabolome-profile.png)"
   ]
  }
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