update for CCD.

STOmics · Nov 22, 2023 · b2ce07f · b2ce07f
1 parent 996a2af
commit b2ce07f
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/stereo/algorithm/ccd/community_clustering_algorithm.py b/stereo/algorithm/ccd/community_clustering_algorithm.py
@@ -276,9 +276,10 @@ def calculate_cell_mixture_stats(self):
         stats_table = {}
         # calculate cell type mixtures for every cluster
         for label, cluster_data in cell_types_communities.groupby(clustering_labels):
-            cell_type_dict = {ct: 0 for ct in self.unique_cell_type}
-            for cell in cluster_data[self.annotation]:
-                cell_type_dict[cell] += 1
+            # cell_type_dict = {ct: 0 for ct in self.unique_cell_type}
+            # for cell in cluster_data[self.annotation]:
+            #     cell_type_dict[cell] += 1
+            cell_type_dict = {ct: np.sum(cluster_data[self.annotation] == ct) for ct in self.unique_cell_type}
 
             # remove excluded cell types
             cell_type_dict = {k: cell_type_dict[k] for k in self.tissue.var.index.sort_values()}

diff --git a/stereo/algorithm/ccd/utils.py b/stereo/algorithm/ccd/utils.py
@@ -86,7 +86,7 @@ def reset_figure_params():
         for key in rcParams.keys():
             if key in original_rcParams:
                 rcParams[key] = original_rcParams[key]
-        original_rcParams = None
+        # original_rcParams = None
 
 
 def csv_to_anndata(csv_file_path: str, annotation: str):

diff --git a/stereo/algorithm/community_detection.py b/stereo/algorithm/community_detection.py
@@ -304,7 +304,8 @@ def cluster(self, merged_tissue):  # TODO, merged_tissue da bude AnnBasedStereoE
         merged_tissue = AnnBasedStereoExpData(h5ad_file_path=None, based_ann_data=merged_tissue)
         if self.params['cluster_algo'] == 'leiden':
             merged_tissue._ann_data.obsm['X_pca_dummy'] = merged_tissue._ann_data.X
-            merged_tissue.tl.neighbors(pca_res_key='X_pca_dummy', n_neighbors=15)
+            merged_tissue.tl.neighbors(pca_res_key='X_pca_dummy', n_neighbors=15,
+                                       n_jobs=-1, res_key='neighbors')
             merged_tissue.tl.leiden(neighbors_res_key='neighbors', res_key='leiden',
                                     resolution=self.params['resolution'])
             merged_tissue._ann_data.obs['leiden'] = merged_tissue._ann_data.obs['leiden'].astype('int')
@@ -752,6 +753,7 @@ def plot(self, function_ind: str, slice_id=0, community_id=None):
         finally:
             self.params['hide_plots'] = orig_hide_plots
             self.algo_list[slice_id].hide_plots = orig_hide_plots
+            reset_figure_params()
 
 
 class CommunityDetection(AlgorithmBase, _CommunityDetection):