From 9605ed3cfc618de30f63f9bf290daeb73ec29b13 Mon Sep 17 00:00:00 2001 From: David L Gibbs Date: Wed, 29 Nov 2023 14:35:39 -0800 Subject: [PATCH] test update --- gssnng/test/example_script.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gssnng/test/example_script.py b/gssnng/test/example_script.py index 82aa1be..d2c3d87 100644 --- a/gssnng/test/example_script.py +++ b/gssnng/test/example_script.py @@ -16,19 +16,19 @@ print("scoring cells") score_cells.with_gene_sets( adata=q, - gene_set_file="data/cibersort_lm22.gmt", + gene_set_file="gssnng/gssnng/test/data/cibersort_lm22.gmt", groupby='louvain', smooth_mode='connectivity', recompute_neighbors=0, - score_method="singscore", - method_params={'normalization':'theoretical'}, + score_method="geneset_overlap", + method_params= {'threshold': 0, 'fraction': False}, ranked=True, cores=8 ) t1 = time.time() - print("MEAN SCORES for the T.cells.CD8.up signature") + print("MEAN GENESET OVERLAP for the T.cells.CD8.up signature") print(q.obs.groupby(['louvain'])['T.cells.CD8.up'].mean().reset_index()) print('end time: ' + str(t1)) @@ -38,19 +38,19 @@ print("scoring cells ... again!") score_cells.with_gene_sets( adata=q, - gene_set_file="data/cibersort_lm22.gmt", + gene_set_file="gssnng/gssnng/test/data/cibersort_lm22.gmt", groupby='louvain', smooth_mode='connectivity', recompute_neighbors=0, - score_method="singscore", - method_params={'normalization':'theoretical'}, + score_method="summed_up", + method_params={}, ranked=True, cores=8 ) t2 = time.time() - print("MEAN SCORES for the T.cells.CD8.up signature") + print("MEAN SUMMED_UP SCORES for the T.cells.CD8.up signature") print(q.obs.groupby(['louvain'])['T.cells.CD8.up'].mean().reset_index()) print('end time: ' + str(t1))