Expose different style, transform Nan to 0

bardin-lab · Apr 7, 2020 · 9a6e3f2 · 9a6e3f2
1 parent 5825ef6
commit 9a6e3f2
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Showing 3 changed files with 32 additions and 2 deletions.
diff --git a/galaxy/plot_coverage.xml b/galaxy/plot_coverage.xml
@@ -10,7 +10,7 @@ plot_coverage
     #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
     --file '$r.input' '$identifier' $r.total_reads
 #end for
-output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind
+output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind --style $style
     ]]></command>
     <inputs>
         <repeat name="input_files" title="Add input files to coverage plot" min="1">
@@ -31,6 +31,29 @@ output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_ki
             <option value="area">Area plot</option>
             <option value="line">Line plot</option>
         </param>
+       <param name="style" type="select" label="Select a plotting style">
+           <option value="ggplot">ggplot</option>
+           <option value="classic">classic</option>
+           <option value="greyscale">greyscale</option>
+           <option value="dark_background">dark_background</option>
+           <option value="seaborn">seaborn</option>
+           <option value="seaborn-bright">seaborn-bright</option>
+           <option value="seaborn-colorblind">seaborn-colorblind</option>
+           <option value="seaborn-dark">seaborn-dark</option>
+           <option value="seaborn-dark-palette">seaborn-dark-palette</option>
+           <option value="seaborn-darkgrid">seaborn-darkgrid</option>
+           <option value="seaborn-deep">seaborn-deep</option>
+           <option value="seaborn-muted">seaborn-muted</option>
+           <option value="seaborn-notebook">seaborn-notebook</option>
+           <option value="seaborn-paper">seaborn-paper</option>
+           <option value="seaborn-pastel">seaborn-pastel</option>
+           <option value="seaborn-poster">seaborn-poster</option>
+           <option value="seaborn-talk">seaborn-talk</option>
+           <option value="seaborn-ticks">seaborn-ticks</option>
+           <option value="seaborn-white">seaborn-white</option>
+           <option value="seaborn-whitegrid">seaborn-whitegrid</option>
+           <option value="tableau-colorblind10">tableau-colorblind10</option>
+       </param>
     </inputs>
     <outputs>
         <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>

diff --git a/readtagger/cli/plot_coverage.py b/readtagger/cli/plot_coverage.py
@@ -1,5 +1,6 @@
 import click
 
+from matplotlib.style import available
 from readtagger.plot_coverage import plot_coverage_in_regions
 from readtagger import VERSION
 
@@ -23,6 +24,10 @@
               default='area',
               type=click.Choice(['area', 'line']),
               help='Kind of plot.')
+@click.option('-s',
+              '--style',
+              type=click.Choice(available),
+              default='ggplot')
 @click.version_option(version=VERSION)
 def plot_coverage(**kwargs):
     """Plot coverage differences between file1 and file2."""

diff --git a/readtagger/plot_coverage.py b/readtagger/plot_coverage.py
@@ -85,7 +85,9 @@ def plot_coverage(contigs_coverage, style='ggplot', plot_kind='area', nrows=8):
             figs.append(fig)
         i += 1
         nrow = i - (int(i / nrows) * nrows)
-        ax = pd.DataFrame.from_dict(data).reset_index().plot(
+        df = pd.DataFrame.from_dict(data).reset_index()
+        df = df.sort_values('index').fillna(0)
+        ax = df.plot(
             x='index',
             kind=plot_kind,
             title=title,