Update total diseases analysis.ipynb

analysis/total diseases analysis.ipynb

@@ -111,6 +111,7 @@
     "dis_lcc = {}  # Module size\n",
     "dis_lcc_dp = {}  # Results for statistical validation dp\n",
     "dis_lcc_ndp = {}  # Results for statistical validation ndp\n",
+    "prots_interactome_dict = {} # Disease proteins in interactome\n",
     "\n",
     "dis_total = dis_dru_the['dis'].unique().tolist()\n",
     "\n",
@@ -124,7 +125,8 @@
     "    \n",
     "    # Disease proteins in interactome\n",
     "    prots_interactome = functions_network_medicine_schizo.gen_pro_PPI(prots, pro_pro)\n",
-    "\n",
+    "    prots_interactome_dict[dis] = prots_interactome\n",
+    "    \n",
     "    # Module size\n",
     "    SG_dis = G_ppi.subgraph(prots_interactome)\n",
     "    \n",
@@ -149,9 +151,9 @@
     "results = {\n",
     "    \"ID\": dis_total,\n",
     "    \"Seed genes\": [len(dis_gen_dict[dis]) for dis in dis_total],\n",
-    "    \"Genes in PPI\": [len(dis_total[dis_total[\"dis\"] == dis][\"pro_ppi\"].iloc[0]) for dis in dis_total],\n",
+    "    \"Genes in PPI\": len(prots_interactome_dict[dis]) for dis in dis_total],\n",
     "    \"Genes in LCC\": [len(dis_lcc[dis]) for dis in dis_total],\n",
-    "    \"Relative LCC\": [len(dis_lcc[dis]) / len(dis_total[dis_total[\"dis\"] == dis][\"pro_ppi\"].iloc[0]) for dis in dis_total],\n",
+    "    \"Relative LCC\": [len(dis_lcc[dis]) / len(functions_network_medicine.pro_gen_dict(dis_gen_dict[dis], gen_pro)) if len(functions_network_medicine.pro_gen_dict(dis_gen_dict[dis], gen_pro)) != 0 else 0 for dis in dis_total],\n",
     "    \"Mean random LCC (ndp)\": [dis_lcc_ndp[dis][0] for dis in dis_total],\n",
     "    \"Std random LCC (ndp)\": [dis_lcc_ndp[dis][1] for dis in dis_total],\n",
     "    \"Z-score (ndp)\": [dis_lcc_ndp[dis][2] for dis in dis_total],\n",