updated cmp usage to fit the recent mpl updates. (#1001)

* updated cmp usage to fit the recent mpl updates.

* updated the requirements.txt

deeptools/correlation.py

@@ -1,5 +1,6 @@
 import sys
 import itertools
+import copy
 import numpy as np
 import scipy.cluster.hierarchy as sch
 import scipy.stats
@@ -291,7 +292,7 @@ def plot_correlation(self, plot_filename, plot_title='', vmax=None,
                                link_color_func=lambda k: 'darkred')
         axdendro.set_xticks([])
         axdendro.set_yticks([])
-        cmap = plt.get_cmap(colormap)
+        cmap = copy.copy(plt.get_cmap(colormap))
 
         # this line simply makes a new cmap, based on the original
         # colormap that goes from 0.0 to 0.9

deeptools/correlation_heatmap.py

@@ -6,6 +6,7 @@
 import scipy.cluster.hierarchy as sch
 from matplotlib import rcParams
 import matplotlib.colors as pltcolors
+import copy
 
 rcParams['pdf.fonttype'] = 42
 rcParams['svg.fonttype'] = 'none'
@@ -43,7 +44,7 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,
                            link_color_func=lambda k: 'darkred')
     axdendro.set_xticks([])
     axdendro.set_yticks([])
-    cmap = plt.get_cmap(colormap)
+    cmap = copy.copy(plt.get_cmap(colormap))
 
     # this line simply makes a new cmap, based on the original
     # colormap that goes from 0.0 to 0.9

deeptools/plotHeatmap.py

@@ -9,17 +9,17 @@
 matplotlib.use('Agg')
 matplotlib.rcParams['pdf.fonttype'] = 42
 matplotlib.rcParams['svg.fonttype'] = 'none'
-from deeptools import cm  # noqa: F401
 import matplotlib.pyplot as plt
 from matplotlib.font_manager import FontProperties
 import matplotlib.gridspec as gridspec
 from matplotlib import ticker
-
+import copy
 import sys
 import plotly.offline as py
 import plotly.graph_objs as go
 
 # own modules
+from deeptools import cm  # noqa: F401
 from deeptools import parserCommon
 from deeptools import heatmapper
 from deeptools.heatmapper_utilities import plot_single, plotly_single
@@ -477,7 +477,8 @@ def plotMatrix(hm, outFileName,
     if colorMapDict['colorMap']:
         cmap = []
         for color_map in colorMapDict['colorMap']:
-            cmap.append(plt.get_cmap(color_map))
+            copy_cmp = copy.copy(plt.get_cmap(color_map))
+            cmap.append(copy_cmp)
             cmap[-1].set_bad(colorMapDict['missingDataColor'])  # nans are printed using this color
 
     if colorMapDict['colorList'] and len(colorMapDict['colorList']) > 0:
@@ -529,7 +530,6 @@ def plotMatrix(hm, outFileName,
     else:
         color_list = cmap_plot(np.arange(numgroups) / numgroups)
     alpha = colorMapDict['alpha']
-
     if image_format == 'plotly':
         return plotlyMatrix(hm,
                             outFileName,
@@ -735,7 +735,7 @@ def plotMatrix(hm, outFileName,
                         col = sample
                     ax = fig.add_subplot(grids[-1, col])
                     tick_locator = ticker.MaxNLocator(nbins=3)
-                    cbar = fig.colorbar(img, cax=ax, alpha=alpha, orientation='horizontal', ticks=tick_locator)
+                    cbar = fig.colorbar(img, cax=ax, orientation='horizontal', ticks=tick_locator)
                     labels = cbar.ax.get_xticklabels()
                     ticks = cbar.ax.get_xticks()
                     if ticks[0] == 0:
@@ -759,15 +759,15 @@ def plotMatrix(hm, outFileName,
             grid_start = 0
 
         ax = fig.add_subplot(grids[grid_start:, -1])
-        fig.colorbar(img, cax=ax, alpha=alpha)
+        fig.colorbar(img, cax=ax)
 
     if box_around_heatmaps:
         plt.subplots_adjust(wspace=0.10, hspace=0.025, top=0.85, bottom=0, left=0.04, right=0.96)
     else:
         #  When no box is plotted the space between heatmaps is reduced
         plt.subplots_adjust(wspace=0.05, hspace=0.01, top=0.85, bottom=0, left=0.04, right=0.96)
 
-    plt.savefig(outFileName, bbox_inches='tight', pdd_inches=0, dpi=dpi, format=image_format)
+    plt.savefig(outFileName, bbox_inches='tight', pad_inches=0.1, dpi=dpi, format=image_format)
     plt.close()
 
 

requirements.txt

@@ -1,6 +1,6 @@
 numpy>=1.9.0
 scipy>=0.17.0
-matplotlib>=3.1.0
+matplotlib>=3.3.0
 pysam>=0.14.0
 py2bit>=0.2.0
 numpydoc>=0.5

setup.py

@@ -84,7 +84,7 @@ def openREADME():
     install_requires=[
         "numpy >= 1.9.0",
         "scipy >= 0.17.0",
-        "matplotlib >= 3.1.0",
+        "matplotlib >= 3.3.0",
         "pysam >= 0.14.0",
         "numpydoc >= 0.5",
         "pyBigWig >= 0.2.1",