fix -omics tutorial

nitzanlab · May 3, 2024 · a40e7f8 · a40e7f8
1 parent 921bde6
commit a40e7f8
Showing 1 changed file with 0 additions and 89 deletions.
diff --git a/docs/tutorials/biolord_omics.ipynb b/docs/tutorials/biolord_omics.ipynb
@@ -480,95 +480,6 @@
     "adata_emb = adata_emb[np.concatenate(idx)]"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'adata_preds' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-15-51b7e9f00b20>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpca\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0madata_preds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0msc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mneighbors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0madata_preds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0msc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtl\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mumap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0madata_preds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'adata_preds' is not defined"
-     ]
-    }
-   ],
-   "source": [
-    "sc.pp.pca(adata_preds)\n",
-    "sc.pp.neighbors(adata_preds)\n",
-    "sc.tl.umap(adata_preds)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "adata_preds.obs[\"status_control_counter\"] = adata_preds.obs[\"status_control\"].copy()\n",
-    "adata_preds.obs[\"status_control_counter\"] = adata_preds.obs[\"status_control_counter\"].cat.rename_categories(\n",
-    "    {\"Infected\": \"Infected (c-pred.)\", \"Uninfected\": \"Uninfected (c-pred.)\"}\n",
-    ")\n",
-    "\n",
-    "adata_preds.uns[\"status_control_counter_colors\"] = [\"#bdc3c7\", \"#f01313\", \"#6f8e32\"]\n",
-    "\n",
-    "size = 4\n",
-    "fig, axs = plt.subplots(1, 2, figsize=(2 * (size + 1), size))\n",
-    "\n",
-    "for i, c in enumerate([\"status_control_counter\", \"zone\"]):\n",
-    "    sc.pl.umap(adata_preds, color=[c], ax=axs[i], show=False)\n",
-    "\n",
-    "    axs[i].set_axis_off()\n",
-    "\n",
-    "plt.tight_layout()\n",
-    "plt.show()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "scores_genes_ttest = {}\n",
-    "for gene in adata_source.var_names:\n",
-    "    res = ttest_rel(\n",
-    "        a=adata_preds[adata_preds.obs[\"status_control\"] == \"Infected\", gene].X,\n",
-    "        b=adata_preds[adata_preds.obs[\"status_control\"] == \"Control\", gene].X,\n",
-    "    )\n",
-    "\n",
-    "    scores_genes_ttest[gene] = {\"statistic\": res.statistic[0], \"pvalue\": res.pvalue[0]}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "df_pvalue = pd.DataFrame.from_dict(scores_genes_ttest).T\n",
-    "df_pvalue.head()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 16,