Update clustermap.py

wanglab-broad · Aug 8, 2022 · b68b92f · b68b92f
1 parent c2b5cac
commit b68b92f
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/ClusterMap/clustermap.py b/ClusterMap/clustermap.py
@@ -84,7 +84,7 @@ def __init__(self, spots, gene_list, dapi=None, num_dims=3, xy_radius=None,z_rad
         self.cellcenter = None
 
     def preprocess(self,dapi_grid_interval=5, LOF=False, contamination=0.1, pct_filter=0.1):
-        preprocessing_data(self.spots, dapi_grid_interval, self.dapi_binary, LOF,contamination, self.xy_radius,pct_filter)
+        self.spots = preprocessing_data(self.spots, dapi_grid_interval, self.dapi_binary, LOF,contamination, self.xy_radius,pct_filter)
 
     def segmentation(self,cell_num_threshold=0.01, dapi_grid_interval=5, add_dapi=True,use_genedis=True):
 
@@ -796,4 +796,4 @@ def discover_subclusters(self, resol_gene, resol_niche, n_neighbors):
             ari = adjusted_rand_score(adata_g.obs['subclusters'], adata_n.obs['niche_subclusters'])
             print(f'Adjusted Rand index for cell type {ct} = {ari}')
 
-            ari_list.append(ari)
+            ari_list.append(ari)