Implement #924 (#925)

* Basic implementation of --linesAtTickMarks and galaxy wrapper

* bump version to 3.4.0

* typo

* stupid eigenvalues

CHANGES.txt

@@ -1,3 +1,8 @@
+3.4.0
+
+ * Fixed a bug in one of the Galaxy wrappers.
+ * Added the `--lineAtTickMarks` option to `plotHeatmap` so that there are dashed vertical lines for each tick mark in the plot. (issue #924)
+
 3.3.2
 
  * Fixed --yAxisLabel in plotProfile (issue #889)

deeptools/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.3.2'
+__version__ = '3.4.0'

deeptools/parserCommon.py

@@ -611,6 +611,12 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
                               'example: --sortUsingSamples 1 3',
                               type=int, nargs='+')
 
+        optional.add_argument('--linesAtTickMarks',
+                              help='Draw dashed lines from all tick marks through the heatmap. '
+                              'This is then similar to the dashed line draw at region bounds '
+                              'when using a reference point and --sortUsing region_length',
+                              action='store_true')
+
         optional.add_argument('--clusterUsingSamples',
                               help='List of sample numbers (order as in '
                               'matrix), that are used for clustering by '

deeptools/plotHeatmap.py

@@ -389,6 +389,7 @@ def plotMatrix(hm, outFileName,
                heatmapWidth=7.5,
                perGroup=False, whatToShow='plot, heatmap and colorbar',
                plot_type='lines',
+               linesAtTickMarks=False,
                image_format=None,
                legend_location='upper-left',
                box_around_heatmaps=True,
@@ -659,6 +660,18 @@ def plotMatrix(hm, outFileName,
             elif not perGroup and sample == 0:
                 ax.axes.set_ylabel(sub_matrix['group'])
 
+            # Plot vertical lines at tick marks if desired
+            if linesAtTickMarks:
+                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]
+                else:
+                    xticks_heat_use = xticks_heat
+                for x in xticks_heat_use:
+                    ax.axvline(x=x, color='black', linewidth=0.5, dashes=(3, 2))
+
             # add labels to last block in a column
             if (perGroup and sample == numsamples - 1) or \
                (not perGroup and group_idx == numgroups - 1):
@@ -845,6 +858,7 @@ def main(args=None):
                args.heatmapWidth,
                args.perGroup,
                args.whatToShow,
+               linesAtTickMarks=args.linesAtTickMarks,
                plot_type=args.plotType,
                image_format=args.plotFileFormat,
                legend_location=args.legendLocation,

galaxy/wrapper/deepTools_macros.xml

@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.3.2.0</token>
+    <token name="@WRAPPER_VERSION@">3.4.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.3.2">deeptools</requirement>
+            <requirement type="package" version="3.4.0">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />

galaxy/wrapper/plotHeatmap.xml

@@ -34,6 +34,10 @@
                     --sortRegions '$advancedOpt.sortRegions'
                 #end if
 
+                #if $advancedOpt.linesAtTickMarks:
+                    --linesAtTickMarks
+                #end if
+
                 #if $advancedOpt.sortUsing:
                     --sortUsing '$advancedOpt.sortUsing'
                 #end if
@@ -130,6 +134,8 @@
             <when value="yes">
                 <expand macro="sortRegions" />
                 <expand macro="sortUsing" />
+                <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
+                    label="Draw dashed lines in heatmap above all tick marks?" />
                 <param argument="--averageTypeSummaryPlot" type="select"
                     label="Type of statistic that should be plotted in the summary image above the heatmap"
                     help="">

galaxy/wrapper/test-data/plotPCA_result2.tabular

@@ -1,4 +1,4 @@
 #plotPCA --outFileNameData
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
 1	-0.7071067811865476	-0.7071067811865475	4.0
-2	-0.7071067811865475	0.7071067811865476	2.49319462166397e-32
+2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32