clean n_genes defaults

scverse · Jun 16, 2020 · 9a41c1a · 9a41c1a
1 parent c01917e
commit 9a41c1a
Showing 1 changed file with 2 additions and 4 deletions.
diff --git a/scanpy/tools/_rank_genes_groups.py b/scanpy/tools/_rank_genes_groups.py
@@ -520,17 +520,15 @@ def rank_genes_groups(
     # for clarity, rename variable
     n_genes_user = n_genes
     # make sure indices are not OoB in case there are less genes than n_genes
-    if n_genes_user is not None and n_genes_user > test_obj.X.shape[1]:
+    # defaults to all genes
+    if n_genes_user is None or n_genes_user > test_obj.X.shape[1]:
         n_genes_user = test_obj.X.shape[1]
 
     ns = np.count_nonzero(test_obj.groups_masks, axis=1)
     logg.debug(f'consider {groupby!r} groups:')
     logg.debug(f'with sizes: {ns}')
     del ns
 
-    # all genes with sorted scores and names for every group
-    n_genes_user = 0 if n_genes_user is None else n_genes_user
-
     test_obj.compute_statistics(method, corr_method, n_genes_user, rankby_abs, **kwds)
 
     if test_obj.pts is not None: