deeptools · dpryan79 · Sep 3, 2019 · Aug 26, 2019 · Aug 26, 2019 · Aug 26, 2019
diff --git a/.azure-pipelines/test-template.yml b/.azure-pipelines/test-template.yml
@@ -1,9 +1,9 @@
 steps:
-- bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython
+- bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals
   displayName: Installing dependencies
 - bash: |
     source activate foo
-    python setup.py install
+    python -m pip install . --no-deps --ignore-installed -vvv
   displayName: Installing deeptools
 - bash: |
     source activate foo

diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,9 @@
+3.3.1
+
+ * Fixed compatibility with matplotlib 3
+ * The Y-axis labels should once again appear in both plotHeatmap and plotProfile (issue #844). This was related to the previous point.
+ * Testing is no longer performed with python 2.7, which will reach end of life in a couple months
+
 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/azure-pipelines.yml b/azure-pipelines.yml
@@ -8,8 +8,6 @@ jobs:
     vmImage: 'ubuntu-16.04'
   strategy:
     matrix:
-      Python27:
-        python.version: '2.7'
       Python37:
         python.version: '3.7'
     maxParallel: 4
@@ -24,8 +22,6 @@ jobs:
     vmImage: 'macOS-10.13'
   strategy:
     matrix:
-      Python27:
-        python.version: '2.7'
       Python37:
         python.version: '3.7'
     maxParallel: 1
@@ -54,7 +50,7 @@ jobs:
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
    displayName: Add conda to PATH
-  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython planemo setuptools
+  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals planemo samtools
     displayName: Installing dependencies
   - bash: |
       source activate foo

diff --git a/deeptools/heatmapper_utilities.py b/deeptools/heatmapper_utilities.py
@@ -126,6 +126,8 @@ def getProfileTicks(hm, referencePointLabel, startLabel, endLabel, idx):
     correspond to the heatmap
 
     As of deepTools 3, the various parameters can be lists, in which case we then need to index things (the idx parameter)
+
+    As of matplotlib 3 the ticks in the heatmap need to have 0.5 added to them.
     """
     w = hm.parameters['bin size']
     b = hm.parameters['upstream']
@@ -164,7 +166,6 @@ def getProfileTicks(hm, referencePointLabel, startLabel, endLabel, idx):
         xtickslabel = ['{0:.1f}'.format(-(float(b) / quotient)),
                        referencePointLabel,
                        '{0:.1f}{1}'.format(float(a) / quotient, symbol)]
-
     else:
         xticks_values = [0]
         xtickslabel = []
@@ -194,7 +195,6 @@ def getProfileTicks(hm, referencePointLabel, startLabel, endLabel, idx):
             xtickslabel.append('{0:.1f}{1}'.format(float(a) / quotient, symbol))
 
         xticks = [(k / w) - tickPlotAdj for k in xticks_values]
-
-    xticks = [max(x, 0.5) for x in xticks]
+        xticks = [max(x, 0) for x in xticks]
 
     return xticks, xtickslabel
diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
@@ -665,6 +665,7 @@ def plotMatrix(hm, outFileName,
                 # add xticks to the bottom heatmap (last group)
                 ax.axes.get_xaxis().set_visible(True)
                 xticks_heat, xtickslabel_heat = hm.getTicks(sample)
+                xticks_heat = [x + 0.5 for x in xticks_heat]  # There's an offset of 0.5 compared to the profile plot
                 if np.ceil(max(xticks_heat)) != float(sub_matrix['matrix'].shape[1]):
                     tickscale = float(sub_matrix['matrix'].shape[1]) / max(xticks_heat)
                     xticks_heat_use = [x * tickscale for x in xticks_heat]

diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
@@ -559,6 +559,8 @@ def plot_heatmap(self):
                 ax.axes.set_yticklabels(labels[::-1])
             else:
                 ax.axes.set_yticklabels([])
+            # matplotlib 3.1.1 (and likely some earlier versions) will change the ylim if you change the tick locations!
+            ax.axes.set_ylim([ymin, ymax])
 
             ax_list.append(ax)
 
@@ -743,14 +745,9 @@ def plot_profile(self):
             globalYmin = min(np.float64(globalYmin), ax.get_ylim()[0])
             globalYmax = max(globalYmax, ax.get_ylim()[1])
 
-            # remove the numbers of the y axis for all plots
-            plt.setp(ax.get_yticklabels(), visible=False)
-
-            if col == 0 or len(self.y_min) > 1 or len(self.y_max) > 1:
-                # add the y axis label for the first plot
-                # on each row and make the numbers and ticks visible
-                plt.setp(ax.get_yticklabels(), visible=True)
-                ax.axes.set_ylabel(self.y_axis_label)
+            # Exclude ticks from all but one subplot by default
+            if col > 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
+                plt.setp(ax.get_yticklabels(), visible=False)
 
             totalWidth = sub_matrix['matrix'].shape[1]
             xticks, xtickslabel = self.getTicks(tickIdx)

diff --git a/deeptools/test/test_heatmapper/heatmap_master_multi_color.png b/deeptools/test/test_heatmapper/heatmap_master_multi_color.png
diff --git a/deeptools/test/test_heatmapper/heatmap_master_multi_colormap_no_box.png b/deeptools/test/test_heatmapper/heatmap_master_multi_colormap_no_box.png
diff --git a/deeptools/test/test_heatmapper/master.png b/deeptools/test/test_heatmapper/master.png
diff --git a/deeptools/test/test_heatmapper/master_relabeled.png b/deeptools/test/test_heatmapper/master_relabeled.png
diff --git a/deeptools/test/test_heatmapper/master_scale_reg.png b/deeptools/test/test_heatmapper/master_scale_reg.png
diff --git a/deeptools/test/test_heatmapper/profile_master.png b/deeptools/test/test_heatmapper/profile_master.png
diff --git a/deeptools/test/test_heatmapper/profile_master_multi.png b/deeptools/test/test_heatmapper/profile_master_multi.png
diff --git a/deeptools/test/test_heatmapper/profile_master_multi_pergroup.png b/deeptools/test/test_heatmapper/profile_master_multi_pergroup.png
diff --git a/deeptools/test/testskip_heatmapper_images.py b/deeptools/test/testskip_heatmapper_images.py
@@ -1,4 +1,6 @@
 import os
+import matplotlib
+matplotlib.use('Agg')
 from matplotlib.testing.compare import compare_images
 from tempfile import NamedTemporaryFile
 
@@ -12,6 +14,10 @@
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_heatmapper/"
 tolerance = 30
 
+skip = False
+if matplotlib.__version__ != "3.1.1":
+    skip = True
+
 
 def test_plotHeatmap_simple_plot():
     """
@@ -22,6 +28,8 @@ def test_plotHeatmap_simple_plot():
       -R {test_path}/test.bed -o /tmp/mat.gz -bs 25
 
     """
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master.mat.gz --outFileName {}".format(ROOT, outfile.name).split()
     deeptools.plotHeatmap.main(args)
@@ -31,6 +39,8 @@ def test_plotHeatmap_simple_plot():
 
 
 def test_plotHeatmap_rename_labels():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
 
     args = "-m {}/master.mat.gz --outFileName {} --regionsLabel uno dos".format(ROOT, outfile.name).split()
@@ -41,6 +51,8 @@ def test_plotHeatmap_rename_labels():
 
 
 def test_plotHeatmap_scale_regions():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_scale_reg.mat.gz --outFileName {}".format(ROOT, outfile.name).split()
     deeptools.plotHeatmap.main(args)
@@ -50,6 +62,8 @@ def test_plotHeatmap_scale_regions():
 
 
 def test_plotHeatmap_multi_bigwig_pergroup():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_multi.mat.gz --perGroup --samplesLabel file1 file2 file3 file4 " \
            "--outFileName {}".format(ROOT, outfile.name).split()
@@ -60,6 +74,8 @@ def test_plotHeatmap_multi_bigwig_pergroup():
 
 
 def test_plotHeatmap_multiple_colors_muti_scales():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_multi.mat.gz --colorList white,blue white,red --zMin 1 0 --zMax 4 5 " \
            "--outFileName {}".format(ROOT, outfile.name).split()
@@ -70,6 +86,8 @@ def test_plotHeatmap_multiple_colors_muti_scales():
 
 
 def test_plotHeatmap_multiple_colormap_no_boxes():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_multi.mat.gz --colorMap Reds binary terrain --boxAroundHeatmaps no " \
            "--outFileName {}".format(ROOT, outfile.name).split()
@@ -80,6 +98,8 @@ def test_plotHeatmap_multiple_colormap_no_boxes():
 
 
 def test_plotHeatmap_interpolation():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/large_matrix.mat.gz --interpolation bilinear " \
            "--outFileName {}".format(ROOT, outfile.name).split()
@@ -90,6 +110,8 @@ def test_plotHeatmap_interpolation():
 
 
 def test_plotProfiler():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master.mat.gz --outFileName {} --regionsLabel uno dos " \
            "--plotType std".format(ROOT, outfile.name).split()
@@ -100,6 +122,8 @@ def test_plotProfiler():
 
 
 def test_plotProfiler_heatmap():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master.mat.gz --outFileName {} --plotType heatmap".format(ROOT, outfile.name).split()
     deeptools.plotProfile.main(args)
@@ -109,6 +133,8 @@ def test_plotProfiler_heatmap():
 
 
 def test_plotProfiler_overlapped_lines():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master.mat.gz --outFileName {} " \
            "--plotType overlapped_lines --yMin -1".format(ROOT, outfile.name).split()
@@ -119,6 +145,8 @@ def test_plotProfiler_overlapped_lines():
 
 
 def test_plotProfiler_multibigwig():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_multi.mat.gz --outFileName {} " \
            "--numPlotsPerRow 2 --yMax 1.5".format(ROOT, outfile.name).split()
@@ -129,6 +157,8 @@ def test_plotProfiler_multibigwig():
 
 
 def test_plotProfiler_multibigwig_pergroup():
+    if skip:
+        return
     outfile = NamedTemporaryFile(suffix='.png', prefix='plotHeatmap_test_', delete=False)
     args = "-m {}/master_multi.mat.gz --outFileName {} " \
            "--perGroup --yMax 1.5".format(ROOT, outfile.name).split()

diff --git a/galaxy/wrapper/test-data/heatmapper_result1.png b/galaxy/wrapper/test-data/heatmapper_result1.png
diff --git a/galaxy/wrapper/test-data/heatmapper_result2.png b/galaxy/wrapper/test-data/heatmapper_result2.png
diff --git a/galaxy/wrapper/test-data/test.bw b/galaxy/wrapper/test-data/test.bw
diff --git a/galaxy/wrapper/test-data/test.bw b/galaxy/wrapper/test-data/test.bw
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 numpy>=1.9.0
 scipy>=0.17.0
-matplotlib>=2.1.2
+matplotlib>=3.0.0
 pysam>=0.14.0
 py2bit>=0.2.0
 numpydoc>=0.5

diff --git a/setup.py b/setup.py
@@ -84,7 +84,7 @@ def openREADME():
     install_requires=[
         "numpy >= 1.9.0",
         "scipy >= 0.17.0",
-        "matplotlib >= 2.1.2",
+        "matplotlib >= 3.0.0",
         "pysam >= 0.14.0",
         "numpydoc >= 0.5",
         "pyBigWig >= 0.2.1",