6.compare-rephetio.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Rephetio DWPCs: compare hetmech values with Cypher values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pathlib\n",
    "\n",
    "import pandas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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>compound_id</th>\n",
       "      <th>disease_id</th>\n",
       "      <th>metapath</th>\n",
       "      <th>cypher_dwpc</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:10283</td>\n",
       "      <td>CbG&lt;rG&lt;rGaD</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:10534</td>\n",
       "      <td>CbG&lt;rG&lt;rGaD</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  compound_id  disease_id     metapath  cypher_dwpc\n",
       "0     DB00014  DOID:10283  CbG<rG<rGaD          0.0\n",
       "1     DB00014  DOID:10534  CbG<rG<rGaD          0.0"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "commit = 'ef5f7a6b76b6a01499d65b95e3d7ca93ac5aba57'\n",
    "url = f'https://github.com/dhimmel/learn/raw/{commit}/all-features/data/matrix/dwpc.tsv.bz2'\n",
    "cypher_df = (\n",
    "    pandas.read_table(url)\n",
    "    .query(\"hetnet == 'rephetio-v2.0'\")\n",
    "    .drop('hetnet', axis='columns')\n",
    "    .melt(id_vars=['compound_id', 'disease_id'], var_name='metapath', value_name='cypher_dwpc')\n",
    ")\n",
    "cypher_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>compound_id</th>\n",
       "      <th>disease_id</th>\n",
       "      <th>metapath</th>\n",
       "      <th>matrix_dwpc</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:0050156</td>\n",
       "      <td>CbGaD</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:0050425</td>\n",
       "      <td>CbGaD</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  compound_id    disease_id metapath  matrix_dwpc\n",
       "0     DB00014  DOID:0050156    CbGaD          0.0\n",
       "1     DB00014  DOID:0050425    CbGaD          0.0"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "path = pathlib.Path('data/rephetio-DWPCs-hetmech.tsv.xz')\n",
    "matrix_df = (\n",
    "    pandas.read_table(path, compression='xz')\n",
    "    .rename(columns={'compound': 'compound_id', 'disease': 'disease_id'})\n",
    "    .melt(id_vars=['compound_id', 'disease_id'], var_name='metapath', value_name='matrix_dwpc')\n",
    ")\n",
    "matrix_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "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>compound_id</th>\n",
       "      <th>disease_id</th>\n",
       "      <th>metapath</th>\n",
       "      <th>cypher_dwpc</th>\n",
       "      <th>matrix_dwpc</th>\n",
       "      <th>difference</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:10283</td>\n",
       "      <td>CbG&lt;rG&lt;rGaD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DB00014</td>\n",
       "      <td>DOID:10534</td>\n",
       "      <td>CbG&lt;rG&lt;rGaD</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  compound_id  disease_id     metapath  cypher_dwpc  matrix_dwpc  difference\n",
       "0     DB00014  DOID:10283  CbG<rG<rGaD          0.0          0.0         0.0\n",
       "1     DB00014  DOID:10534  CbG<rG<rGaD          0.0          0.0         0.0"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "compare_df = cypher_df.merge(matrix_df)\n",
    "compare_df['difference'] = (compare_df.cypher_dwpc - compare_df.matrix_dwpc).abs()\n",
    "compare_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fbce97f2438>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib inline\n",
    "compare_df.difference.hist();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1.0000000000037756e-05"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "max(compare_df['difference'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>compound_id</th>\n",
       "      <th>disease_id</th>\n",
       "      <th>metapath</th>\n",
       "      <th>cypher_dwpc</th>\n",
       "      <th>matrix_dwpc</th>\n",
       "      <th>difference</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>3798851</th>\n",
       "      <td>DB00570</td>\n",
       "      <td>DOID:1612</td>\n",
       "      <td>CuGdAdGdD</td>\n",
       "      <td>0.18177</td>\n",
       "      <td>0.18176</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2290157</th>\n",
       "      <td>DB00996</td>\n",
       "      <td>DOID:1826</td>\n",
       "      <td>CpDpCtD</td>\n",
       "      <td>0.13992</td>\n",
       "      <td>0.13991</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1519936</th>\n",
       "      <td>DB00970</td>\n",
       "      <td>DOID:1909</td>\n",
       "      <td>CdGeAeGdD</td>\n",
       "      <td>0.20717</td>\n",
       "      <td>0.20718</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>209375</th>\n",
       "      <td>DB00755</td>\n",
       "      <td>DOID:1192</td>\n",
       "      <td>CbGbCtD</td>\n",
       "      <td>0.15368</td>\n",
       "      <td>0.15369</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4306626</th>\n",
       "      <td>DB01204</td>\n",
       "      <td>DOID:1612</td>\n",
       "      <td>CuGuCdGaD</td>\n",
       "      <td>0.14017</td>\n",
       "      <td>0.14016</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3978779</th>\n",
       "      <td>DB08865</td>\n",
       "      <td>DOID:8893</td>\n",
       "      <td>CuGeAeGdD</td>\n",
       "      <td>0.24277</td>\n",
       "      <td>0.24278</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3211271</th>\n",
       "      <td>DB00997</td>\n",
       "      <td>DOID:1192</td>\n",
       "      <td>CtDlAlDrD</td>\n",
       "      <td>0.13528</td>\n",
       "      <td>0.13529</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4270358</th>\n",
       "      <td>DB00445</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>CuGuAeGuD</td>\n",
       "      <td>0.13237</td>\n",
       "      <td>0.13236</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1537992</th>\n",
       "      <td>DB00694</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>CdGeAuGdD</td>\n",
       "      <td>0.14663</td>\n",
       "      <td>0.14664</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4108403</th>\n",
       "      <td>DB00570</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>CuGpBPpGdD</td>\n",
       "      <td>0.15948</td>\n",
       "      <td>0.15949</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2858525</th>\n",
       "      <td>DB00451</td>\n",
       "      <td>DOID:12306</td>\n",
       "      <td>CrCtDrD</td>\n",
       "      <td>0.20358</td>\n",
       "      <td>0.20359</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1993521</th>\n",
       "      <td>DB00270</td>\n",
       "      <td>DOID:10763</td>\n",
       "      <td>CiPCiCrCtD</td>\n",
       "      <td>0.17597</td>\n",
       "      <td>0.17596</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4272057</th>\n",
       "      <td>DB00997</td>\n",
       "      <td>DOID:2531</td>\n",
       "      <td>CuGuAeGuD</td>\n",
       "      <td>0.13237</td>\n",
       "      <td>0.13236</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3961852</th>\n",
       "      <td>DB00783</td>\n",
       "      <td>DOID:10283</td>\n",
       "      <td>CuGeAdGaD</td>\n",
       "      <td>0.16478</td>\n",
       "      <td>0.16479</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1065321</th>\n",
       "      <td>DB00441</td>\n",
       "      <td>DOID:1459</td>\n",
       "      <td>CdG&lt;rGeAlD</td>\n",
       "      <td>0.12707</td>\n",
       "      <td>0.12706</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3274249</th>\n",
       "      <td>DB00620</td>\n",
       "      <td>DOID:8893</td>\n",
       "      <td>CtDrD</td>\n",
       "      <td>0.21402</td>\n",
       "      <td>0.21403</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1993817</th>\n",
       "      <td>DB00381</td>\n",
       "      <td>DOID:10763</td>\n",
       "      <td>CiPCiCrCtD</td>\n",
       "      <td>0.17597</td>\n",
       "      <td>0.17596</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2861136</th>\n",
       "      <td>DB01583</td>\n",
       "      <td>DOID:12306</td>\n",
       "      <td>CrCtDrD</td>\n",
       "      <td>0.20358</td>\n",
       "      <td>0.20359</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3038360</th>\n",
       "      <td>DB01248</td>\n",
       "      <td>DOID:363</td>\n",
       "      <td>CtDaGeAlD</td>\n",
       "      <td>0.11883</td>\n",
       "      <td>0.11884</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3202385</th>\n",
       "      <td>DB00563</td>\n",
       "      <td>DOID:9008</td>\n",
       "      <td>CtDlAeGuD</td>\n",
       "      <td>0.11857</td>\n",
       "      <td>0.11856</td>\n",
       "      <td>0.00001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        compound_id  disease_id    metapath  cypher_dwpc  matrix_dwpc  \\\n",
       "3798851     DB00570   DOID:1612   CuGdAdGdD      0.18177      0.18176   \n",
       "2290157     DB00996   DOID:1826     CpDpCtD      0.13992      0.13991   \n",
       "1519936     DB00970   DOID:1909   CdGeAeGdD      0.20717      0.20718   \n",
       "209375      DB00755   DOID:1192     CbGbCtD      0.15368      0.15369   \n",
       "4306626     DB01204   DOID:1612   CuGuCdGaD      0.14017      0.14016   \n",
       "3978779     DB08865   DOID:8893   CuGeAeGdD      0.24277      0.24278   \n",
       "3211271     DB00997   DOID:1192   CtDlAlDrD      0.13528      0.13529   \n",
       "4270358     DB00445   DOID:2531   CuGuAeGuD      0.13237      0.13236   \n",
       "1537992     DB00694   DOID:2531   CdGeAuGdD      0.14663      0.14664   \n",
       "4108403     DB00570   DOID:2531  CuGpBPpGdD      0.15948      0.15949   \n",
       "2858525     DB00451  DOID:12306     CrCtDrD      0.20358      0.20359   \n",
       "1993521     DB00270  DOID:10763  CiPCiCrCtD      0.17597      0.17596   \n",
       "4272057     DB00997   DOID:2531   CuGuAeGuD      0.13237      0.13236   \n",
       "3961852     DB00783  DOID:10283   CuGeAdGaD      0.16478      0.16479   \n",
       "1065321     DB00441   DOID:1459  CdG<rGeAlD      0.12707      0.12706   \n",
       "3274249     DB00620   DOID:8893       CtDrD      0.21402      0.21403   \n",
       "1993817     DB00381  DOID:10763  CiPCiCrCtD      0.17597      0.17596   \n",
       "2861136     DB01583  DOID:12306     CrCtDrD      0.20358      0.20359   \n",
       "3038360     DB01248    DOID:363   CtDaGeAlD      0.11883      0.11884   \n",
       "3202385     DB00563   DOID:9008   CtDlAeGuD      0.11857      0.11856   \n",
       "\n",
       "         difference  \n",
       "3798851     0.00001  \n",
       "2290157     0.00001  \n",
       "1519936     0.00001  \n",
       "209375      0.00001  \n",
       "4306626     0.00001  \n",
       "3978779     0.00001  \n",
       "3211271     0.00001  \n",
       "4270358     0.00001  \n",
       "1537992     0.00001  \n",
       "4108403     0.00001  \n",
       "2858525     0.00001  \n",
       "1993521     0.00001  \n",
       "4272057     0.00001  \n",
       "3961852     0.00001  \n",
       "1065321     0.00001  \n",
       "3274249     0.00001  \n",
       "1993817     0.00001  \n",
       "2861136     0.00001  \n",
       "3038360     0.00001  \n",
       "3202385     0.00001  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "compare_df.sort_values('difference', ascending=False).head(20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Series([], Name: metapath, dtype: int64)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Metapaths\n",
    "compare_df.query(\"difference > 0.01\").metapath.value_counts()"
   ]
  }
 ],
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