check var index names

DendrouLab · Apr 11, 2024 · 1550212 · 1550212
1 parent b3d366b
commit 1550212
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/panpipes/python_scripts/run_cell2location.py b/panpipes/python_scripts/run_cell2location.py
@@ -266,6 +266,8 @@
 cell2loc_plot_QC_reference(model_ref, figdir + "/QC_reference_reconstruction_accuracy.png", figdir + "/QC_reference_expression signatures_vs_avg_expression.png")
 
 # save model and update mudata
+if adata_sc.var.index.names[0] in adata_sc.var.columns: 
+	adata_sc.var.index.names = [None]
 mdata_singlecell.mod["rna"] = adata_sc
 mdata_singlecell.update()
 if save_models is True:
@@ -301,6 +303,8 @@
 
 
 # save model and update mudata
+if adata_st.var.index.names[0] in adata_st.var.columns: 
+	adata_st.var.index.names = [None]
 mdata_spatial.mod["spatial"] = adata_st
 mdata_spatial.update()
 if save_models is True: