diff --git a/src/funki/analysis.py b/src/funki/analysis.py index 061d0cc..723c18f 100644 --- a/src/funki/analysis.py +++ b/src/funki/analysis.py @@ -1,6 +1,7 @@ import scanpy as sc import anndata as ad import decoupler as dc +from decoupler.decouple import parse_methods from pydeseq2.dds import DeseqDataSet, DefaultInference from pydeseq2.ds import DeseqStats @@ -60,6 +61,10 @@ def enrich( erated/decoupler.decouple.html#decoupler.decouple ''' + # Using methods parser from Decoupler before storing config + # This prevents e.g. storing `None` when running with default methods + methods = parse_methods(methods)[0] + # Storing parameters data.uns['funki']['enrich'] = { 'methods': methods,