make sc columns categorical

openproblems-bio · Oct 17, 2024 · 5400682 · 5400682
1 parent 214d513
commit 5400682
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/src/process_dataset/split_sc/script.py b/src/process_dataset/split_sc/script.py
@@ -50,6 +50,9 @@
 filtered_sc_counts.uns.clear()
 filtered_sc_counts.obsm.clear()
 filtered_sc_counts.obsp.clear()
+for col in filtered_sc_counts.obs.columns:
+    if col not in ["cell_count_by_well_celltype", "cell_count_by_plate_well", "obs_id"]:
+        filtered_sc_counts.obs[col] = filtered_sc_counts.obs[col].astype("category")
 
 print(">> Save sc dataset into splits", flush=True)
 filtered_sc_counts[filtered_sc_counts.obs["split"] == "train"].write_h5ad(par["sc_train_h5ad"], compression="gzip")