Update graph_construct.py

dance/transforms/graph_construct.py

@@ -12,6 +12,7 @@
 import sklearn
 import torch
 from dgl import nn as dglnn
+import scipy.stats
 from scipy import sparse as sp
 from scipy.sparse import csc_matrix
 from scipy.spatial import distance, distance_matrix, minkowski_distance
@@ -276,7 +277,18 @@ def construct_pathway_graph(gex_data, **kwargs):
                         if j != k:
                             uu.append(j)
                             vv.append(k)
-                            ee.append(corr[j][k])
+                            ee.append(1-corr[j][k])
+        elif pww == 'spearman':
+            spe=scipy.stats.spearmanr(gex_features.toarray())[0]
+            if gex_features.toarray().shape[0]==2:
+                spe=np.array([[1,spe],[spe,1]])
+            for i in new_pw:
+                for j in i:
+                    for k in i:
+                        if j != k:
+                            uu.append(j)
+                            vv.append(k)
+                            ee.append(1-spe[j][k])
 
         pickle.dump([uu, vv, ee], open(pk_path, 'wb'))