Update isolated_labels.py

theislab · Jan 27, 2023 · f6090be · f6090be
1 parent 1be0daa
commit f6090be
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/scib/metrics/isolated_labels.py b/scib/metrics/isolated_labels.py
@@ -1,5 +1,6 @@
 import pandas as pd
 from sklearn.metrics import f1_score
+from sklearn.metrics import silhouette_samples
 
 from .clustering import cluster_optimal_resolution
 from .silhouette import silhouette
@@ -227,7 +228,8 @@ def max_f1(adata, label_key, cluster_key, label, argmax=False):
     else:
         # AWS score between isolated label vs rest
         adata.obs[iso_label_key] = adata.obs[label_key] == isolated_label
-        score = silhouette(adata, iso_label_key, embed)
+        adata.obs['silhouette_temp'] = silhouette_samples(adata.obsm[embed], adata.obs[iso_label_key])
+        score = adata.obs[adata.obs[iso_label_key]].silhouette_temp.mean()
 
     if verbose:
         print(f"{isolated_label}: {score}")