demo/disease_critical_network.ipynb

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    "## KGWAS Disease critical network\n",
    "This notebook showcases an example to generate (1) KGWAS network weights for each edge, measuring the importance of the edge to explain the disease GWAS signals and (2) variant interpretation graph where for each variant, it retrieves the top K nodes that are most important to explain the GWAS signals of the variant.\n",
    "\n",
    "This code assumes that you have the model folder `./data/model/test` saved. Feel free to modify the path to your own model folder."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "All required data files are present.\n",
      "--loading KG---\n",
      "--using enformer SNP embedding--\n",
      "--using random go embedding--\n",
      "--using ESM gene embedding--\n",
      "Loading example GWAS file...\n",
      "Example file already exists locally.\n",
      "Loading GWAS file from ./data/biochemistry_Creatinine_fastgwa_full_10000_1.fastGWA...\n",
      "Using ldsc weight...\n",
      "ldsc_weight mean:  0.9999999999999993\n",
      "Retrieving weights...\n",
      "Aggregating across node types...\n",
      "Start generating disease critical network...\n",
      "No filters... Using all genes and gene programs...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/dfs/user/kexinh/miniconda3/envs/a100_env/lib/python3.8/site-packages/pandas/core/indexing.py:1773: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  self._setitem_single_column(ilocs[0], value, pi)\n",
      "/dfs/user/kexinh/miniconda3/envs/a100_env/lib/python3.8/site-packages/pandas/core/indexing.py:1667: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  self.obj[key] = value\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Disease critical network finished generating...\n",
      "Generating variant interpretation networks...\n",
      "Number of hit snps:  3\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 3/3 [00:22<00:00,  7.50s/it]\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('../')\n",
    "\n",
    "from kgwas import KGWAS, KGWAS_Data\n",
    "data = KGWAS_Data(data_path = './data/')\n",
    "data.load_kg()\n",
    "\n",
    "data.load_external_gwas(example_file = True)\n",
    "data.process_gwas_file()\n",
    "data.prepare_split()\n",
    "\n",
    "run = KGWAS(data, device = 'cuda:9', exp_name = 'test')\n",
    "run.load_pretrained('./data/model/test')\n",
    "df_network_weight, df_variant_interpretation, disease_critical_network = run.get_disease_critical_network(variant_threshold = 5e-8, \n",
    "                                                                                                            magma_path = None, magma_threshold = 0.05, program_threshold = 0.05,\n",
    "                                                                                                            K_neighbors = 3, num_cpus = 1)"
   ]
  },
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>1016826</th>\n",
       "      <td>16746.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>0.312869</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Reaction</td>\n",
       "      <td>RAB14</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>443769</th>\n",
       "      <td>7132.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>-0.000451</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Literature</td>\n",
       "      <td>GABARAP</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3204</th>\n",
       "      <td>1938.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>-0.034033</td>\n",
       "      <td>BiologicalProcess</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Associates</td>\n",
       "      <td>Glycogen catabolic process</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34520</th>\n",
       "      <td>17247.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>-0.034096</td>\n",
       "      <td>BiologicalProcess</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Associates</td>\n",
       "      <td>Glycophagy</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29598</th>\n",
       "      <td>13657.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>-0.034503</td>\n",
       "      <td>BiologicalProcess</td>\n",
       "      <td>Gene</td>\n",
       "      <td>Associates</td>\n",
       "      <td>Intracellular transport</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449552</th>\n",
       "      <td>197686.0</td>\n",
       "      <td>18584.0</td>\n",
       "      <td>2.281075</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs6829573</td>\n",
       "      <td>SHROOM3</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449272</th>\n",
       "      <td>197568.0</td>\n",
       "      <td>18584.0</td>\n",
       "      <td>1.772625</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs6836365</td>\n",
       "      <td>SHROOM3</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449497</th>\n",
       "      <td>197656.0</td>\n",
       "      <td>18584.0</td>\n",
       "      <td>1.618933</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs55650799</td>\n",
       "      <td>SHROOM3</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449256</th>\n",
       "      <td>197565.0</td>\n",
       "      <td>2909.0</td>\n",
       "      <td>1.428451</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs17319721</td>\n",
       "      <td>CCDC158</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449433</th>\n",
       "      <td>197621.0</td>\n",
       "      <td>2909.0</td>\n",
       "      <td>1.427075</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs1493360</td>\n",
       "      <td>CCDC158</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449317</th>\n",
       "      <td>197577.0</td>\n",
       "      <td>2909.0</td>\n",
       "      <td>1.374755</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs60871166</td>\n",
       "      <td>CCDC158</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>448552</th>\n",
       "      <td>197443.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>1.292024</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs7697073</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>448562</th>\n",
       "      <td>197444.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>1.273231</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs79146874</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>448575</th>\n",
       "      <td>197445.0</td>\n",
       "      <td>19980.0</td>\n",
       "      <td>1.256691</td>\n",
       "      <td>SNP</td>\n",
       "      <td>Gene</td>\n",
       "      <td>PCHi-C</td>\n",
       "      <td>rs12498327</td>\n",
       "      <td>STBD1</td>\n",
       "      <td>rs13146355</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            h_idx     t_idx  importance             h_type t_type  \\\n",
       "393735     4238.0  115005.0    0.707107               Gene    SNP   \n",
       "1098740   17670.0    4238.0    1.779486               Gene   Gene   \n",
       "573324     8800.0    4238.0    0.425998               Gene   Gene   \n",
       "786046    13187.0    4238.0    0.019682               Gene   Gene   \n",
       "28855     13165.0    4238.0   -0.035167  BiologicalProcess   Gene   \n",
       "30283     14457.0    4238.0   -0.035197  BiologicalProcess   Gene   \n",
       "14116      6294.0    4238.0   -0.035242  BiologicalProcess   Gene   \n",
       "280494   114935.0    4238.0    1.473419                SNP   Gene   \n",
       "280526   114958.0    4238.0    1.433980                SNP   Gene   \n",
       "280523   114956.0    4238.0    1.381602                SNP   Gene   \n",
       "1611316   18584.0  197572.0    1.394467               Gene    SNP   \n",
       "260136     2909.0  197572.0    0.884753               Gene    SNP   \n",
       "1729186   19980.0  197572.0    0.856848               Gene    SNP   \n",
       "1122286   17788.0   18584.0   -0.000446               Gene   Gene   \n",
       "1164822   18443.0   18584.0   -0.000453               Gene   Gene   \n",
       "333210     5512.0   18584.0   -0.000456               Gene   Gene   \n",
       "491797     7839.0    2909.0    0.628518               Gene   Gene   \n",
       "1169157   18527.0    2909.0    0.563372               Gene   Gene   \n",
       "430656     6932.0    2909.0   -0.000444               Gene   Gene   \n",
       "1249313   20031.0   19980.0    0.457000               Gene   Gene   \n",
       "1016826   16746.0   19980.0    0.312869               Gene   Gene   \n",
       "443769     7132.0   19980.0   -0.000451               Gene   Gene   \n",
       "3204       1938.0   19980.0   -0.034033  BiologicalProcess   Gene   \n",
       "34520     17247.0   19980.0   -0.034096  BiologicalProcess   Gene   \n",
       "29598     13657.0   19980.0   -0.034503  BiologicalProcess   Gene   \n",
       "449552   197686.0   18584.0    2.281075                SNP   Gene   \n",
       "449272   197568.0   18584.0    1.772625                SNP   Gene   \n",
       "449497   197656.0   18584.0    1.618933                SNP   Gene   \n",
       "449256   197565.0    2909.0    1.428451                SNP   Gene   \n",
       "449433   197621.0    2909.0    1.427075                SNP   Gene   \n",
       "449317   197577.0    2909.0    1.374755                SNP   Gene   \n",
       "448552   197443.0   19980.0    1.292024                SNP   Gene   \n",
       "448562   197444.0   19980.0    1.273231                SNP   Gene   \n",
       "448575   197445.0   19980.0    1.256691                SNP   Gene   \n",
       "\n",
       "                    rel_type                            h_id        t_id  \\\n",
       "393735                  Exon                            CPS1   rs1047891   \n",
       "1098740  PhysicalAssociation                           RPL35        CPS1   \n",
       "573324   PhysicalAssociation                           HSPA5        CPS1   \n",
       "786046       DosageLethality                             MYC        CPS1   \n",
       "28855             Associates  Nitric oxide metabolic process        CPS1   \n",
       "30283             Associates  Homocysteine metabolic process        CPS1   \n",
       "14116             Associates  Triglyceride catabolic process        CPS1   \n",
       "280494                PCHi-C                     rs116492934        CPS1   \n",
       "280526                PCHi-C                     rs148584272        CPS1   \n",
       "280523                PCHi-C                     rs138424013        CPS1   \n",
       "1611316                  VEP                         SHROOM3  rs13146355   \n",
       "260136                  eQTL                         CCDC158  rs13146355   \n",
       "1729186                 eQTL                           STBD1  rs13146355   \n",
       "1122286           Literature                         RPS6KA1     SHROOM3   \n",
       "1164822           Literature                             SFN     SHROOM3   \n",
       "333210            Literature                          DYNLL1     SHROOM3   \n",
       "491797   PhysicalAssociation                           GPSM1     CCDC158   \n",
       "1169157            Signaling                         SH3GLB2     CCDC158   \n",
       "430656            Literature                             FOS     CCDC158   \n",
       "1249313             Reaction                            STOM       STBD1   \n",
       "1016826             Reaction                           RAB14       STBD1   \n",
       "443769            Literature                         GABARAP       STBD1   \n",
       "3204              Associates      Glycogen catabolic process       STBD1   \n",
       "34520             Associates                      Glycophagy       STBD1   \n",
       "29598             Associates         Intracellular transport       STBD1   \n",
       "449552                PCHi-C                       rs6829573     SHROOM3   \n",
       "449272                PCHi-C                       rs6836365     SHROOM3   \n",
       "449497                PCHi-C                      rs55650799     SHROOM3   \n",
       "449256                PCHi-C                      rs17319721     CCDC158   \n",
       "449433                PCHi-C                       rs1493360     CCDC158   \n",
       "449317                PCHi-C                      rs60871166     CCDC158   \n",
       "448552                PCHi-C                       rs7697073       STBD1   \n",
       "448562                PCHi-C                      rs79146874       STBD1   \n",
       "448575                PCHi-C                      rs12498327       STBD1   \n",
       "\n",
       "          QUERY_SNP  \n",
       "393735    rs1047891  \n",
       "1098740   rs1047891  \n",
       "573324    rs1047891  \n",
       "786046    rs1047891  \n",
       "28855     rs1047891  \n",
       "30283     rs1047891  \n",
       "14116     rs1047891  \n",
       "280494    rs1047891  \n",
       "280526    rs1047891  \n",
       "280523    rs1047891  \n",
       "1611316  rs13146355  \n",
       "260136   rs13146355  \n",
       "1729186  rs13146355  \n",
       "1122286  rs13146355  \n",
       "1164822  rs13146355  \n",
       "333210   rs13146355  \n",
       "491797   rs13146355  \n",
       "1169157  rs13146355  \n",
       "430656   rs13146355  \n",
       "1249313  rs13146355  \n",
       "1016826  rs13146355  \n",
       "443769   rs13146355  \n",
       "3204     rs13146355  \n",
       "34520    rs13146355  \n",
       "29598    rs13146355  \n",
       "449552   rs13146355  \n",
       "449272   rs13146355  \n",
       "449497   rs13146355  \n",
       "449256   rs13146355  \n",
       "449433   rs13146355  \n",
       "449317   rs13146355  \n",
       "448552   rs13146355  \n",
       "448562   rs13146355  \n",
       "448575   rs13146355  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_variant_interpretation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In default, it does not use any filtering on the genes and programs. But we highly suggest you do so! You can do it by simply feeding the MAGMA result file to `magma_path`. For how to run MAGMA, check out [this notebook](run_magma.ipynb)!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": []
  }
 ],
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