shorter comments

Author: LevyNat

spatial/scVIVA_tutorial.ipynb

@@ -322,10 +322,10 @@
    "outputs": [],
    "source": [
     "setup_kwargs = {\n",
-    "    \"sample_key\": \"sample\",  # specify column in adata.obs that contains the individual slide ID\n",
-    "    \"labels_key\": \"cell_type\",  # specify column in adata.obs that contains the cell type labels\n",
-    "    \"cell_coordinates_key\": \"spatial\",  # specify key in adata.obsm that contains the spatial coordinates\n",
-    "    \"expression_embedding_key\": \"X_scANVI\",  # specify key in adata.obsm that contains the expression embedding\n",
+    "    \"sample_key\": \"sample\",  # column in adata.obs that contains the individual slide ID\n",
+    "    \"labels_key\": \"cell_type\",  # column in adata.obs that contains the cell type labels\n",
+    "    \"cell_coordinates_key\": \"spatial\",  # spatial coordinates key in adata.obsm\n",
+    "    \"expression_embedding_key\": \"X_scANVI\",  # expression embedding key in adata.obsm\n",
     "}"
    ]
   },
@@ -410,8 +410,8 @@
    "source": [
     "scvi.external.SCVIVA.setup_anndata(\n",
     "    adata,\n",
-    "    layer=\"counts\",  # specify layer in adata that contains the raw counts\n",
-    "    batch_key=\"sample\",  # specify column in adata.obs that contains the batch covariate to correct for\n",
+    "    layer=\"counts\",  # adata layer that contains the raw counts\n",
+    "    batch_key=\"sample\",  # column in adata.obs that contains the batch covariate\n",
     "    **setup_kwargs,\n",
     ")"
    ]