Fix #493

Author: dpryan79

CHANGES.txt

@@ -1,3 +1,8 @@
+2.4.3
+
+ * Fixed incorrect label ordering in the `plotCorrelation` command with the `--outFileCorMatrix` options.
+ * Fixed bug #491, which involved python 3 and bamCoverage.
+
 2.4.2
 
  * Fixed an issue where `computeMatrix reference-point --referencePoint center` would break if 1-base regions were used. This was bug #456.

deeptools/correlation.py

@@ -161,7 +161,7 @@ def save_corr_matrix(self, file_handle):
         saves the correlation matrix
         """
         if self.column_order:
-            self.corr_matrix[self.column_order, self.column_order]
+            self.corr_matrix = self.corr_matrix[:, self.column_order][self.column_order]
             self.labels = [self.labels[i] for i in self.column_order]
 
         file_handle.write("\t'" + "'\t'".join(self.labels) + "'\n")