adjust code to use regular ndarray instead of matrix subclass which wil be deprecated

pathways/pathways_relevance.py

@@ -207,8 +207,9 @@ class PathwaysScores(object):
             ax = plt.gca()
 
 
-        im, cbar = util.heatmap(data = genes_in_pathways_and_scores_df.as_matrix(),
-                                row_labels = genes_in_pathways_and_scores_df.index.values, col_labels=pathways_significant_names,
+        im, cbar = util.heatmap(data = genes_in_pathways_and_scores_df.values,
+                                row_labels = genes_in_pathways_and_scores_df.index.values,
+                                col_labels=pathways_significant_names,
                                 ax=ax, cbar_kw = {'shrink':0.15, 'orientation':'vertical'},
                                 cmap="YlGn", cbarlabel="Gene score")