fix #838

deeptools · Jun 26, 2019 · abdd70d · abdd70d
1 parent ecce499
commit abdd70d
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,7 @@
+3.3.1
+
+ * Fixed `--plotNumbers` not working in `plotCorrelation`. This was issue #838
+
 3.3.0
 
  * `plotCoverage` now has a `--BED` option, to restrict plots and output to apply to a specific set of regions given by a BED or GTF file or files (issue #829).

diff --git a/deeptools/correlation.py b/deeptools/correlation.py
@@ -299,8 +299,8 @@ def plot_correlation(self, plot_filename, plot_title='', vmax=None,
         # a good contrast between the correlation numbers that are
         # plotted on black.
         if plot_numbers:
-            cmap = cmap.from_list(colormap + "clipped",
-                                  cmap(np.linspace(0, 0.9, 10)))
+            cmap = plt_colors.LinearSegmentedColormap.from_list(colormap + "clipped",
+                                                                cmap(np.linspace(0, 0.9, 10)))
 
         cmap.set_under((0., 0., 1.))
         # Plot distance matrix.

diff --git a/deeptools/correlation_heatmap.py b/deeptools/correlation_heatmap.py
@@ -4,6 +4,7 @@
 import numpy as np
 import scipy.cluster.hierarchy as sch
 from matplotlib import rcParams
+import matplotlib.colors as pltcolors
 
 rcParams['pdf.fonttype'] = 42
 rcParams['svg.fonttype'] = 'none'
@@ -50,8 +51,8 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,
     # a good contrast between the correlation numbers that are
     # plotted on black.
     if plot_numbers:
-        cmap = cmap.from_list(colormap + "clipped",
-                              cmap(np.linspace(0, 0.9, 10)))
+        cmap = plt_colors.LinearSegmentedColormap.from_list(colormap + "clipped",
+                                                            cmap(np.linspace(0, 0.9, 10)))
 
     cmap.set_under((0., 0., 1.))
     # Plot distance matrix.