concat pd before writing to a file

ebi-gene-expression-group · Dec 13, 2023 · f72770c · f72770c
1 parent ba18fbd
commit f72770c
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py
@@ -95,7 +95,10 @@
 
 if args.output is not None:
     # write adata.obsm[mlm_key] and adata.obsm[mlm_pvals_key] to the output network files
-    adata.obsm["mlm_estimate", "mlm_pvals"].to_csv(args.output + "_mlm.tsv", sep="\t")
+    combined_df = pd.concat([adata.obsm["mlm_estimate"], adata.obsm["mlm_pvals"]], axis=1)
+
+    # Save the combined dataframe to a file
+    combined_df.to_csv(args.output + "_mlm.tsv", sep="\t")
 
 # if args.activities_path is specified, generate the activities AnnData and save the AnnData object to the specified path
 if args.activities_path is not None: