enforce column vector in consolidate

Genentech · Sep 12, 2024 · 1c46f1e · 1c46f1e
1 parent f20818d
commit 1c46f1e
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/src/scimilarity/utils.py b/src/scimilarity/utils.py
@@ -221,7 +221,9 @@ def consolidate_duplicate_symbols(
     dup_genes_data = []
     for k in dup_genes:
         idx = [i for i, x in enumerate(adata.var.index.values) if x == k]
-        counts = csr_matrix(adata.layers["counts"][:, idx].sum(axis=1))
+        counts = csr_matrix(
+            np.array(adata.layers["counts"][:, idx].sum(axis=1)).flatten()[:, None]
+        )
         gene_data = anndata.AnnData(
             X=csr_matrix(counts.shape),
             var=pd.DataFrame(index=[k]),