Merge branch 'scottgigante-patch-5'

theislab · May 13, 2022 · bdb2b05 · bdb2b05
2 parents 8a38aa5 + 3178239
commit bdb2b05
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scib/preprocessing.py b/scib/preprocessing.py
@@ -290,7 +290,7 @@ def normalize(
     if precluster:
         # Preliminary clustering for differentiated normalisation
         adata_pp = adata.copy()
-        sc.pp.normalize_per_cell(adata_pp, counts_per_cell_after=1e6)
+        sc.pp.normalize_per_cell(adata_pp, counts_per_cell_after=1e6, min_counts=1)
         sc.pp.log1p(adata_pp)
         sc.pp.pca(adata_pp, n_comps=15, svd_solver="arpack")
         sc.pp.neighbors(adata_pp)