revert changes of latent_to_gene.py

JianYang-Lab · Oct 28, 2024 · 7f7f54e · 7f7f54e
1 parent 9220c00
commit 7f7f54e
Showing 1 changed file with 1 addition and 4 deletions.
diff --git a/src/gsMap/latent_to_gene.py b/src/gsMap/latent_to_gene.py
@@ -96,7 +96,7 @@ def find_neighbors_regional(cell_pos, spatial_net_dict, coor_latent, config, cel
 
 
 def compute_regional_mkscore(cell_pos, spatial_net_dict, coor_latent, config, cell_annotations,
-                             ranks, frac_whole, adata_X_bool, eps=1e-10):
+                             ranks, frac_whole, adata_X_bool):
     """
     Compute gmean ranks of a region.
     """
@@ -110,13 +110,10 @@ def compute_regional_mkscore(cell_pos, spatial_net_dict, coor_latent, config, ce
     ranks_tg = ranks[cell_select_pos, :]
     gene_ranks_region = gmean(ranks_tg, axis=0)
     gene_ranks_region[gene_ranks_region <= 1] = 0
-    mask = (frac_whole < eps)
-    frac_whole[mask] = 1
 
     if not config.no_expression_fraction:
         # Ratio of expression fractions
         frac_focal = adata_X_bool[cell_select_pos, :].sum(axis=0).A1 / len(cell_select_pos)
-        # print(f"frac_focal: {frac_focal} | type: {type(frac_focal)}")
         frac_region = frac_focal / frac_whole
         frac_region[frac_region <= 1] = 0
         frac_region[frac_region > 1] = 1