Mutation Frequency Hierarchies.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Applying genetic alteration data to hierarchies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ndex2\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import os\n",
    "import matplotlib.pyplot as plt\n",
    "from cyjupyter import Cytoscape\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Name: NeST Map - Main Model\n",
      "Nodes: 395\n",
      "Edges: 466\n",
      "Node Attributes: 9799\n",
      "Edge Attributes: 881\n",
      "\n"
     ]
    }
   ],
   "source": [
    "NETWORK_UUID = \"9a8f5326-aa6e-11ea-aaef-0ac135e8bacf\"\n",
    "SERVER = \"https://ndexbio.org\"\n",
    "test_network = ndex2.create_nice_cx_from_server(SERVER, uuid=NETWORK_UUID)\n",
    "test_network.print_summary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "#os.getcwd()\n",
    "mutation_file=os.path.join(os.path.abspath(''), \"bc_all_mutations.txt\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene</th>\n",
       "      <th>MutSig(Q-value)</th>\n",
       "      <th># Mut</th>\n",
       "      <th>#</th>\n",
       "      <th>Profiled Samples</th>\n",
       "      <th>Freq</th>\n",
       "      <th>Is Cancer Gene (source: OncoKB)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>FAM200B</td>\n",
       "      <td>NaN</td>\n",
       "      <td>16</td>\n",
       "      <td>16</td>\n",
       "      <td>3102</td>\n",
       "      <td>0.5%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>STPG2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>1282</td>\n",
       "      <td>0.2%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>KRT6C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7</td>\n",
       "      <td>7</td>\n",
       "      <td>2606</td>\n",
       "      <td>0.3%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>INSL3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>1573</td>\n",
       "      <td>0.2%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ASPM</td>\n",
       "      <td>NaN</td>\n",
       "      <td>114</td>\n",
       "      <td>94</td>\n",
       "      <td>4474</td>\n",
       "      <td>2.1%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18378</th>\n",
       "      <td>OCRL</td>\n",
       "      <td>NaN</td>\n",
       "      <td>40</td>\n",
       "      <td>38</td>\n",
       "      <td>4249</td>\n",
       "      <td>0.9%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18379</th>\n",
       "      <td>INPP1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>2501</td>\n",
       "      <td>0.2%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18380</th>\n",
       "      <td>ODF1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>3532</td>\n",
       "      <td>0.3%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18381</th>\n",
       "      <td>ODF2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>44</td>\n",
       "      <td>40</td>\n",
       "      <td>4227</td>\n",
       "      <td>0.9%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18382</th>\n",
       "      <td>CXCL10</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>2865</td>\n",
       "      <td>0.1%</td>\n",
       "      <td>No</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>18383 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          Gene  MutSig(Q-value)  # Mut   #  Profiled Samples  Freq  \\\n",
       "0      FAM200B              NaN     16  16              3102  0.5%   \n",
       "1        STPG2              NaN      3   3              1282  0.2%   \n",
       "2        KRT6C              NaN      7   7              2606  0.3%   \n",
       "3        INSL3              NaN      3   3              1573  0.2%   \n",
       "4         ASPM              NaN    114  94              4474  2.1%   \n",
       "...        ...              ...    ...  ..               ...   ...   \n",
       "18378     OCRL              NaN     40  38              4249  0.9%   \n",
       "18379    INPP1              NaN      6   6              2501  0.2%   \n",
       "18380     ODF1              NaN     11  11              3532  0.3%   \n",
       "18381     ODF2              NaN     44  40              4227  0.9%   \n",
       "18382   CXCL10              NaN      3   3              2865  0.1%   \n",
       "\n",
       "      Is Cancer Gene (source: OncoKB)  \n",
       "0                                  No  \n",
       "1                                  No  \n",
       "2                                  No  \n",
       "3                                  No  \n",
       "4                                  No  \n",
       "...                               ...  \n",
       "18378                              No  \n",
       "18379                              No  \n",
       "18380                              No  \n",
       "18381                              No  \n",
       "18382                              No  \n",
       "\n",
       "[18383 rows x 7 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## the mutation data\n",
    "bc_mutations = pd.read_csv(mutation_file, sep=\"\\t\")\n",
    "bc_mutations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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