From f91fe484c5d367ad0e1618d97865041073cbd543 Mon Sep 17 00:00:00 2001 From: Kangcheng Hou Date: Fri, 24 Nov 2023 12:47:17 -0800 Subject: [PATCH] toy adata n_obs = 30, use sc.pp.neighbors(n_pcs=n_obs - 1) to avoid the reported errors --- tests/test_method_downstream.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_method_downstream.py b/tests/test_method_downstream.py index 006494a..c8a6868 100644 --- a/tests/test_method_downstream.py +++ b/tests/test_method_downstream.py @@ -33,7 +33,7 @@ def test_downstream_group_analysis(): adata, df_cov, df_gs, dic_res_ref = load_toy_data() df_full_score = dic_res_ref["REF_COV_FULL"] - sc.pp.neighbors(adata, n_neighbors=10, n_pcs=40) + sc.pp.neighbors(adata, n_neighbors=10, n_pcs=min(40, adata.n_obs - 1)) dic_res = scdrs.method.downstream_group_analysis( adata, df_full_score, ["cell_type"] @@ -118,7 +118,7 @@ def test_gearys_c(): """ adata, df_cov, df_gs, dic_res_ref = load_toy_data() - sc.pp.neighbors(adata, n_neighbors=10, n_pcs=40) + sc.pp.neighbors(adata, n_neighbors=10, n_pcs=min(40, adata.n_obs - 1)) v_x = np.arange(adata.shape[0]) gc = scdrs.method.gearys_c(adata, v_x)