Fix the --hclust option. As is, scipy was trying to calculate the euc…

…lidean distance of an array of euclidean distances!

deeptools/heatmapper.py

@@ -1077,14 +1077,10 @@ def hmcluster(self, k, method='kmeans'):
 
         if method == 'hierarchical':
             # normally too slow for large data sets
-            from scipy.cluster.hierarchy import fclusterdata
-            from scipy.spatial.distance import pdist
-            print(("the type is ", type(matrix)))
-            print(("original ndim is ", np.asarray(matrix).ndim))
-            foo = pdist(np.asarray(matrix, order='c', dtype=np.double), metric='euclidean')
-            print(("the pdist ndim is ", foo.ndim))
-            del foo
-            cluster_labels = fclusterdata(matrix, k, criterion='maxclust', metric='euclidean', depth=2, method='ward')
+            from scipy.cluster.hierarchy import fcluster, linkage
+            Z = linkage(matrix, method='ward', metric='euclidean')
+            cluster_labels = fcluster(Z, k, criterion='maxclust')
+
         # create groups using the clustering
         self.group_labels = []
         self.group_boundaries = [0]