Merge branch '4.0.0_viz' of github.com:deeptools/deepTools into 4.0.0_viz

Author: Juan Caballero

pydeeptools/deeptools/bamPEFragmentSize.py

@@ -16,7 +16,6 @@
 from deeptools.getFragmentAndReadSize import get_read_and_fragment_length
 from importlib.metadata import version
 
-
 def parse_arguments():
     parser = argparse.ArgumentParser(
         description='This tool calculates the fragment sizes for read pairs given a BAM file from paired-end sequencing.'
@@ -48,7 +47,10 @@ def parse_arguments():
                         'eps, pdf, svg and plotly.',
                         default=None,
                         choices=['png', 'pdf', 'svg', 'eps'])
-
+    parser.add_argument('--ggplot',
+                        help='Use ggplot theme for figures',
+                        action='store_true')
+    
     parser.add_argument('--numberOfProcessors', '-p',
                         help='Number of processors to use. The default is '
                         'to use 1. (Default: %(default)s)',
@@ -307,6 +309,9 @@ def main(args=None):
     if args.table is not None:
         printTable(args, fraglengths, readlengths)
 
+    if args.ggplot:
+        plt.style.use('ggplot')
+
     if args.histogram:
         if args.samplesLabel:
             if len(args.bamfiles) != len(args.samplesLabel):

pydeeptools/deeptools/plotCoverage.py

@@ -16,9 +16,6 @@
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
 
-plt.style.use('ggplot')
-
-
 def parse_arguments(args=None):
     parent_parser = parserCommon.getParentArgParse(binSize=False)
     read_options_parser = parserCommon.read_options()
@@ -104,12 +101,15 @@ def required_args():
                           'the generated image. Leave blank for no title. (Default: %(default)s)',
                           default='')
 
+    optional.add_argument('--ggplot',
+                          help='Use ggplot theme for figures',
+                          action='store_true')
+    
     optional.add_argument('--skipZeros',
                           help='By setting this option, genomic regions '
                           'that have zero or nan values in _all_ samples '
                           'are excluded.',
-                          action='store_true',
-                          required=False)
+                          action='store_true')
 
     optional.add_argument('--numberOfSamples', '-n',
                           help='Number of 1 bp regions to sample. (Default: %(default)s)',
@@ -230,16 +230,11 @@ def main(args=None):
         num_reads_per_bin = countR.remove_row_of_zeros(num_reads_per_bin)
 
     if args.plotFile:
-        if args.plotFileFormat == 'plotly':
-            fig = go.Figure()
-            fig['layout']['xaxis1'] = {'domain': [0.0, 0.48], 'anchor': 'x1', 'title': 'coverage (#reads per base)'}
-            fig['layout']['xaxis2'] = {'domain': [0.52, 1.0], 'anchor': 'x2', 'title': 'coverage (#reads per base)'}
-            fig['layout']['yaxis1'] = {'domain': [0.0, 1.0], 'anchor': 'x1', 'title': 'fraction of bases sampled'}
-            fig['layout']['yaxis2'] = {'domain': [0.0, 1.0], 'anchor': 'x2', 'title': 'fraction of bases sampled >= coverage'}
-            fig['layout'].update(title=args.plotTitle)
-        else:
-            fig, axs = plt.subplots(1, 2, figsize=(args.plotWidth, args.plotHeight))
-            plt.suptitle(args.plotTitle)
+        if args.ggplot:
+            plt.style.use('ggplot')
+
+        fig, axs = plt.subplots(1, 2, figsize=(args.plotWidth, args.plotHeight))
+        plt.suptitle(args.plotTitle)
 
     # plot up to two std from mean
     num_reads_per_bin = num_reads_per_bin.astype(int)

pydeeptools/deeptools/plotFingerprint.py

@@ -125,7 +125,11 @@ def get_optional_args():
                           help='Title of the plot, to be printed on top of '
                           'the generated image. Leave blank for no title. (Default: %(default)s)',
                           default='')
-
+    
+    optional.add_argument('--ggplot',
+                          help='Use ggplot theme for figures',
+                          action='store_true')
+    
     optional.add_argument('--skipZeros',
                           help='If set, then regions with zero overlapping reads'
                           'for *all* given BAM files are ignored. This '
@@ -402,7 +406,8 @@ def main(args=None):
     x = np.arange(total).astype('float') / total  # normalize from 0 to 1
 
     if args.plotFile is not None:
-        plt.style.use('ggplot')
+        if args.ggplot:
+            plt.style.use('ggplot')
 
         i = 0
         # matplotlib won't iterate through line styles by itself

pydeeptools/deeptools/test/test_data/bamPEFragmentSize_histogram_result1.png

@@ -0,0 +1,23 @@
+import os
+import filecmp
+from matplotlib.testing.compare import compare_images
+from tempfile import NamedTemporaryFile
+import deeptools.plotFingerprint
+
+TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotFingerprint/"
+
+print (TEST_DATA)
+print(ROOT)
+tolerance = 13
+
+def test_plotFingerprint_default():
+    plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
+    args = "-b {0}test1.bam {0}test2.bam -o {1} --plotFileFormat png".format(TEST_DATA, plotfile.name).split()
+    deeptools.plotProfile.main(args)
+
+    res = compare_images(ROOT + 'test_plotFingerprint_default.png', plotfile.name, tolerance)
+    
+    assert res is None, res
+    
+    os.remove(plotfile.name)