cell-painting/3.application/lincs_repurposing_moa_analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import os\n",
    "from pycytominer.cyto_utils import infer_cp_features\n",
    "import sys\n",
    "import matplotlib.pyplot as plt\n",
    "sys.path.insert(0, \"../scripts\")\n",
    "from utils import load_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "data_dict = load_data([\"complete\"])\n",
    "meta_features = infer_cp_features(data_dict[\"complete\"], metadata=True)\n",
    "cp_features = infer_cp_features(data_dict[\"complete\"])\n",
    "\n",
    "complete_features_df = data_dict[\"complete\"].reindex(cp_features, axis=\"columns\")\n",
    "complete_meta_df = data_dict[\"complete\"].reindex(meta_features, axis=\"columns\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0        glucocorticoid receptor antagonist\n",
       "1        glucocorticoid receptor antagonist\n",
       "2        glucocorticoid receptor antagonist\n",
       "3        glucocorticoid receptor antagonist\n",
       "4        glucocorticoid receptor antagonist\n",
       "                        ...                \n",
       "10339      progesterone receptor antagonist\n",
       "10340      progesterone receptor antagonist\n",
       "10341      progesterone receptor antagonist\n",
       "10342      progesterone receptor antagonist\n",
       "10343      progesterone receptor antagonist\n",
       "Name: moa, Length: 9408, dtype: object"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#obtain only the moa column from the whole dataframe\n",
    "df = pd.read_csv(\"repurposing_info_external_moa_map_resolved.tsv\",sep='\\t').set_index('broad_sample').reindex(index=complete_meta_df['Metadata_broad_sample']).reset_index().drop('Metadata_broad_sample',axis = 1)\n",
    "moa = df.moa.dropna()\n",
    "moa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "pipes = moa[moa.str.contains(\"\\|\")]\n",
    "unique_pipes = pipes.drop_duplicates()\n",
    "no_pipes = moa[~moa.str.contains(\"\\|\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>full moa occurrence</th>\n",
       "      <th>moa1 occurrence</th>\n",
       "      <th>moa2 occurrence</th>\n",
       "      <th>moa3 occurrence</th>\n",
       "      <th>moa4 occurrence</th>\n",
       "      <th>moa5 occurrence</th>\n",
       "      <th>moa6 occurrence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>30</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144</th>\n",
       "      <td>6</td>\n",
       "      <td>18</td>\n",
       "      <td>6</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>156</th>\n",
       "      <td>66</td>\n",
       "      <td>120</td>\n",
       "      <td>84</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>180</th>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</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>10104</th>\n",
       "      <td>12</td>\n",
       "      <td>6</td>\n",
       "      <td>6</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10134</th>\n",
       "      <td>6</td>\n",
       "      <td>24</td>\n",
       "      <td>6</td>\n",
       "      <td>30.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10164</th>\n",
       "      <td>6</td>\n",
       "      <td>84</td>\n",
       "      <td>84</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10224</th>\n",
       "      <td>6</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10332</th>\n",
       "      <td>6</td>\n",
       "      <td>162</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>170 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       full moa occurrence  moa1 occurrence  moa2 occurrence  moa3 occurrence  \\\n",
       "36                       6                6                0             42.0   \n",
       "48                      30               48               48              NaN   \n",
       "144                      6               18                6              NaN   \n",
       "156                     66              120               84              NaN   \n",
       "180                      6                6                6              NaN   \n",
       "...                    ...              ...              ...              ...   \n",
       "10104                   12                6                6              NaN   \n",
       "10134                    6               24                6             30.0   \n",
       "10164                    6               84               84              NaN   \n",
       "10224                    6               12                0              NaN   \n",
       "10332                    6              162                0              NaN   \n",
       "\n",
       "       moa4 occurrence  moa5 occurrence  moa6 occurrence  \n",
       "36                 NaN              NaN              NaN  \n",
       "48                 NaN              NaN              NaN  \n",
       "144                NaN              NaN              NaN  \n",
       "156                NaN              NaN              NaN  \n",
       "180                NaN              NaN              NaN  \n",
       "...                ...              ...              ...  \n",
       "10104              NaN              NaN              NaN  \n",
       "10134              NaN              NaN              NaN  \n",
       "10164              NaN              NaN              NaN  \n",
       "10224              NaN              NaN              NaN  \n",
       "10332              NaN              NaN              NaN  \n",
       "\n",
       "[170 rows x 7 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#count the number of occurrences of each moa in each moa combination\n",
    "moas_occurences_all_pipes = []\n",
    "for pipe in unique_pipes:\n",
    "    moas = pipe.split(\"|\")\n",
    "    moas_occurences = [pipes[pipes == pipe].count()]\n",
    "    for moa in moas:\n",
    "        moas_occurences.append(no_pipes[no_pipes == moa].count())\n",
    "    moas_occurences_all_pipes.append(moas_occurences)\n",
    "moas_occurrences_all_pipes_df = pd.DataFrame(data=moas_occurences_all_pipes, index = unique_pipes.index.values.tolist(), columns=[\"full moa occurrence\",\"moa1 occurrence\", \"moa2 occurrence\",\"moa3 occurrence\", \"moa4 occurrence\", \"moa5 occurrence\", \"moa6 occurrence\"])\n",
    "moas_occurrences_all_pipes_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>full moa occurrence</th>\n",
       "      <th>moa1 occurrence</th>\n",
       "      <th>moa2 occurrence</th>\n",
       "      <th>moa3 occurrence</th>\n",
       "      <th>moa4 occurrence</th>\n",
       "      <th>moa5 occurrence</th>\n",
       "      <th>moa6 occurrence</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>moa</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>NFkB pathway inhibitor|proteasome inhibitor</th>\n",
       "      <td>330</td>\n",
       "      <td>30</td>\n",
       "      <td>354</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>dopamine receptor antagonist|serotonin receptor antagonist</th>\n",
       "      <td>66</td>\n",
       "      <td>120</td>\n",
       "      <td>84</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cyclooxygenase inhibitor|prostanoid receptor antagonist</th>\n",
       "      <td>30</td>\n",
       "      <td>168</td>\n",
       "      <td>24</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "    <tr>\n",
       "      <th>mTOR inhibitor|PI3K inhibitor</th>\n",
       "      <td>30</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>insulin sensitizer|PPAR receptor agonist</th>\n",
       "      <td>24</td>\n",
       "      <td>18</td>\n",
       "      <td>30</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetylcholinesterase inhibitor|monoamine oxidase inhibitor</th>\n",
       "      <td>6</td>\n",
       "      <td>18</td>\n",
       "      <td>30</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>angiogenesis inhibitor|S100A9 inhibitor</th>\n",
       "      <td>6</td>\n",
       "      <td>24</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cyclooxygenase inhibitor|NFkB pathway inhibitor</th>\n",
       "      <td>6</td>\n",
       "      <td>168</td>\n",
       "      <td>30</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>insulin sensitizer|PPAR receptor partial agonist</th>\n",
       "      <td>6</td>\n",
       "      <td>18</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>adrenergic receptor antagonist|prolactin inhibitor</th>\n",
       "      <td>6</td>\n",
       "      <td>162</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>170 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    full moa occurrence  \\\n",
       "moa                                                                       \n",
       "NFkB pathway inhibitor|proteasome inhibitor                         330   \n",
       "dopamine receptor antagonist|serotonin receptor...                   66   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...                   30   \n",
       "mTOR inhibitor|PI3K inhibitor                                        30   \n",
       "insulin sensitizer|PPAR receptor agonist                             24   \n",
       "...                                                                 ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...                    6   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                               6   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                       6   \n",
       "insulin sensitizer|PPAR receptor partial agonist                      6   \n",
       "adrenergic receptor antagonist|prolactin inhibitor                    6   \n",
       "\n",
       "                                                    moa1 occurrence  \\\n",
       "moa                                                                   \n",
       "NFkB pathway inhibitor|proteasome inhibitor                      30   \n",
       "dopamine receptor antagonist|serotonin receptor...              120   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...              168   \n",
       "mTOR inhibitor|PI3K inhibitor                                    48   \n",
       "insulin sensitizer|PPAR receptor agonist                         18   \n",
       "...                                                             ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...               18   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                          24   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                 168   \n",
       "insulin sensitizer|PPAR receptor partial agonist                 18   \n",
       "adrenergic receptor antagonist|prolactin inhibitor              162   \n",
       "\n",
       "                                                    moa2 occurrence  \\\n",
       "moa                                                                   \n",
       "NFkB pathway inhibitor|proteasome inhibitor                     354   \n",
       "dopamine receptor antagonist|serotonin receptor...               84   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...               24   \n",
       "mTOR inhibitor|PI3K inhibitor                                    48   \n",
       "insulin sensitizer|PPAR receptor agonist                         30   \n",
       "...                                                             ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...               30   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                           0   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                  30   \n",
       "insulin sensitizer|PPAR receptor partial agonist                  0   \n",
       "adrenergic receptor antagonist|prolactin inhibitor                0   \n",
       "\n",
       "                                                    moa3 occurrence  \\\n",
       "moa                                                                   \n",
       "NFkB pathway inhibitor|proteasome inhibitor                     NaN   \n",
       "dopamine receptor antagonist|serotonin receptor...              NaN   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...              NaN   \n",
       "mTOR inhibitor|PI3K inhibitor                                   NaN   \n",
       "insulin sensitizer|PPAR receptor agonist                        NaN   \n",
       "...                                                             ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...              NaN   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                         NaN   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                 NaN   \n",
       "insulin sensitizer|PPAR receptor partial agonist                NaN   \n",
       "adrenergic receptor antagonist|prolactin inhibitor              NaN   \n",
       "\n",
       "                                                    moa4 occurrence  \\\n",
       "moa                                                                   \n",
       "NFkB pathway inhibitor|proteasome inhibitor                     NaN   \n",
       "dopamine receptor antagonist|serotonin receptor...              NaN   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...              NaN   \n",
       "mTOR inhibitor|PI3K inhibitor                                   NaN   \n",
       "insulin sensitizer|PPAR receptor agonist                        NaN   \n",
       "...                                                             ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...              NaN   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                         NaN   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                 NaN   \n",
       "insulin sensitizer|PPAR receptor partial agonist                NaN   \n",
       "adrenergic receptor antagonist|prolactin inhibitor              NaN   \n",
       "\n",
       "                                                    moa5 occurrence  \\\n",
       "moa                                                                   \n",
       "NFkB pathway inhibitor|proteasome inhibitor                     NaN   \n",
       "dopamine receptor antagonist|serotonin receptor...              NaN   \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...              NaN   \n",
       "mTOR inhibitor|PI3K inhibitor                                   NaN   \n",
       "insulin sensitizer|PPAR receptor agonist                        NaN   \n",
       "...                                                             ...   \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...              NaN   \n",
       "angiogenesis inhibitor|S100A9 inhibitor                         NaN   \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                 NaN   \n",
       "insulin sensitizer|PPAR receptor partial agonist                NaN   \n",
       "adrenergic receptor antagonist|prolactin inhibitor              NaN   \n",
       "\n",
       "                                                    moa6 occurrence  \n",
       "moa                                                                  \n",
       "NFkB pathway inhibitor|proteasome inhibitor                     NaN  \n",
       "dopamine receptor antagonist|serotonin receptor...              NaN  \n",
       "cyclooxygenase inhibitor|prostanoid receptor an...              NaN  \n",
       "mTOR inhibitor|PI3K inhibitor                                   NaN  \n",
       "insulin sensitizer|PPAR receptor agonist                        NaN  \n",
       "...                                                             ...  \n",
       "acetylcholinesterase inhibitor|monoamine oxidas...              NaN  \n",
       "angiogenesis inhibitor|S100A9 inhibitor                         NaN  \n",
       "cyclooxygenase inhibitor|NFkB pathway inhibitor                 NaN  \n",
       "insulin sensitizer|PPAR receptor partial agonist                NaN  \n",
       "adrenergic receptor antagonist|prolactin inhibitor              NaN  \n",
       "\n",
       "[170 rows x 7 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "moas_occurrence_df = pd.concat([unique_pipes, moas_occurrences_all_pipes_df],axis = 1)\n",
    "moas_occurrence_df = moas_occurrence_df.sort_values(\"full moa occurrence\", ascending = False)\n",
    "moas_occurrence_df.index = moas_occurrence_df['moa']\n",
    "moas_occurrence_df = moas_occurrence_df.drop('moa',axis =1)\n",
    "moas_occurrence_df.to_csv(\"moas_occurrence.tsv\", sep = \"\\t\")\n",
    "moas_occurrence_df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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