Merge branch 'main' of github.com:inoue0426/drGAT

inoue0426 · Aug 29, 2024 · ec4acf8 · ec4acf8
2 parents a31a732 + 96bc8fa
commit ec4acf8
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Showing 2 changed files with 22 additions and 13 deletions.
diff --git a/Figs/Fig2.ipynb b/Figs/Fig2.ipynb
@@ -1015,7 +1015,7 @@
     }
    ],
    "source": [
-    "len(bubble_data['drug'].unique())"
+    "len(bubble_data[\"drug\"].unique())"
    ]
   },
   {
@@ -1036,7 +1036,7 @@
     }
    ],
    "source": [
-    "len(bubble_data['gene'].unique())"
+    "len(bubble_data[\"gene\"].unique())"
    ]
   },
   {

diff --git a/Figs/preprocess_fig4.ipynb b/Figs/preprocess_fig4.ipynb
@@ -806,7 +806,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df.to_csv('graph_norm.csv')"
+    "df.to_csv(\"graph_norm.csv\")"
    ]
   },
   {
@@ -881,13 +881,17 @@
     "for i in tqdm(res.index):\n",
     "    while True:\n",
     "        try:\n",
-    "            enr = gp.enrichr(gene_list=list(res.loc[i].dropna()[:100]),\n",
-    "                             gene_sets='MSigDB_Hallmark_2020',\n",
-    "                             organism='human',\n",
-    "                             outdir=None)\n",
+    "            enr = gp.enrichr(\n",
+    "                gene_list=list(res.loc[i].dropna()[:100]),\n",
+    "                gene_sets=\"MSigDB_Hallmark_2020\",\n",
+    "                organism=\"human\",\n",
+    "                outdir=None,\n",
+    "            )\n",
     "            tmp = enr.results\n",
-    "            tmp = tmp[tmp['Adjusted P-value'] < 0.05].sort_values(['Adjusted P-value'])[['Term', 'Adjusted P-value', 'Genes']]\n",
-    "            tmp['drug'] = len(tmp)*[i]\n",
+    "            tmp = tmp[tmp[\"Adjusted P-value\"] < 0.05].sort_values([\"Adjusted P-value\"])[\n",
+    "                [\"Term\", \"Adjusted P-value\", \"Genes\"]\n",
+    "            ]\n",
+    "            tmp[\"drug\"] = len(tmp) * [i]\n",
     "            results = pd.concat([results, tmp])\n",
     "            break\n",
     "        except Exception as e:\n",
@@ -903,7 +907,7 @@
    "outputs": [],
    "source": [
     "results.drug = results.drug.astype(int)\n",
-    "results.to_csv('gsea_results.csv')"
+    "results.to_csv(\"gsea_results.csv\")"
    ]
   },
   {
@@ -1251,9 +1255,14 @@
    },
    "outputs": [],
    "source": [
-    "df = results.groupby('Term')['drug'].count().reset_index().merge(results.groupby('Term')['Adjusted P-value'].mean().reset_index())\n",
-    "df = df.sort_values('drug', ascending=False)\n",
-    "df = df[df['drug'] > 10]"
+    "df = (\n",
+    "    results.groupby(\"Term\")[\"drug\"]\n",
+    "    .count()\n",
+    "    .reset_index()\n",
+    "    .merge(results.groupby(\"Term\")[\"Adjusted P-value\"].mean().reset_index())\n",
+    ")\n",
+    "df = df.sort_values(\"drug\", ascending=False)\n",
+    "df = df[df[\"drug\"] > 10]"
    ]
   },
   {