fix for NaN gene_expr value

hubmapconsortium · Nov 28, 2023 · cdba0f9 · cdba0f9
1 parent 4fb1983
commit cdba0f9
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/containers/gene-expression/context/main.py b/containers/gene-expression/context/main.py
@@ -71,6 +71,7 @@ def get_gene_expr(matrix: anndata.AnnData, clid_column: str, gene_expr_column: s
     merged_obs = matrix.obs.merge(
         ct_marker_genes_df[[clid_column, gene_expr_column]], how="left"
     )
+    merged_obs.fillna({gene_expr_column: '[]'}, inplace=True)
     merged_obs[gene_expr_column] = merged_obs[gene_expr_column].apply(json.dumps)
     merged_obs.index = matrix.obs.index
     matrix.obs = merged_obs