tsne split into multiple code cells

volkamerlab · Jan 28, 2025 · faf2594 · faf2594
1 parent 08064e2
commit faf2594
Showing 1 changed file with 41 additions and 9 deletions.
diff --git a/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb b/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb
@@ -1900,24 +1900,56 @@
     "    fragment_library_concat = pd.concat(fragment_library).reset_index(drop=True)\n",
     "fragment_library_concat[\"maccs\"] = fragment_library_concat.ROMol.apply(\n",
     "    MACCSkeys.GenMACCSKeys\n",
-    ")\n",
-    "\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e22eeca4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "pca = PCA(n_components=50)\n",
-    "crds = pca.fit_transform(list(fragment_library_concat[\"maccs\"]))\n",
-    "\n",
+    "crds = pca.fit_transform(list(fragment_library_concat[\"maccs\"]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17fc249a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "crds_embedded = TSNE(\n",
     "    n_components=2, init=\"pca\", learning_rate=\"auto\"\n",
-    ").fit_transform(crds)\n",
-    "\n",
+    ").fit_transform(crds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2bbe496c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "tsne_df = pd.DataFrame(crds_embedded, columns=[\"X\", \"Y\"])\n",
     "# add bool column from filter steps\n",
     "filters = []\n",
     "if \"bool_pains\" in saved_filter_results.columns:\n",
     "    tsne_df[\"pains\"] = saved_filter_results[\"bool_pains\"]\n",
     "    filters.append(\"pains\")\n",
     "\n",
-    "tsne_df[\"smiles\"] = saved_filter_results[\"smiles\"]\n",
-    "\n",
+    "tsne_df[\"smiles\"] = saved_filter_results[\"smiles\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "31a37fc6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "# create the plots for all filters\n",
     "# plt.figure(figsize=(15, 21))\n",
     "i = 0\n",
@@ -1939,7 +1971,7 @@
     "        color=\"lightcoral\",\n",
     "        label=\"rejected\",\n",
     "    )\n",
-    "    plt.show()\n"
+    "    plt.show()"
    ]
   },
   {