From c025b2b086004e7bf9c224cc88b27b709d5e378e Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sun, 23 Apr 2017 22:39:38 +0200
Subject: [PATCH] Implement #508

---
 deeptools/plotCoverage.py           | 17 +++++++++++++----
 galaxy/wrapper/deepTools_macros.xml | 15 +++++++++++++++
 galaxy/wrapper/plotCoverage.xml     |  2 ++
 3 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/deeptools/plotCoverage.py b/deeptools/plotCoverage.py
index ecad83c15..ba8bcea27 100644
--- a/deeptools/plotCoverage.py
+++ b/deeptools/plotCoverage.py
@@ -110,6 +110,16 @@ def required_args():
                           help='Save raw counts (coverages) to file.',
                           metavar='FILE')
 
+    optional.add_argument('--plotHeight',
+                          help='Plot height in cm.',
+                          type=float,
+                          default=5.)
+
+    optional.add_argument('--plotWidth',
+                          help='Plot width in cm. The minimum value is 1 cm.',
+                          type=float,
+                          default=15)
+
     optional.add_argument('--plotFileFormat',
                           metavar='FILETYPE',
                           help='Image format type. If given, this option '
@@ -165,7 +175,7 @@ def main(args=None):
     if args.skipZeros:
         num_reads_per_bin = countR.remove_row_of_zeros(num_reads_per_bin)
 
-    fig, axs = plt.subplots(1, 2, figsize=(15, 5))
+    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)
@@ -212,9 +222,8 @@ def main(args=None):
                                                                   sample_max[idx],
                                                                   ))
 
-    # The 'good' x-axis is computed for each sample. The lower value is favored in which
-    # distributions with a wider x-range can better be seen.
-    y_max = min(y_max)
+    # Don't clip plots
+    y_max = max(y_max)
     axs[0].set_ylim(0, min(1, y_max + (y_max * 0.10)))
     axs[0].set_xlim(0, x_max)
     axs[0].set_xlabel('coverage (#reads per bp)')
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index bff287ffb..d8f40f479 100644
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -25,6 +25,21 @@
         </conditional>
     </xml>
 
+    <token name="@PLOTWIDTHHEIGHT@">
+        --plotWidth '$advancedOp.plotWidth'
+        --plotHeight '$advancedOp.plotHeight'
+    </token>
+
+    <xml name="plotWidthHeight">
+        <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1"
+            label="Plot height"
+            help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
+
+        <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1"
+            label="Plot width"
+            help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
+    </xml>
+
     <token name="@ADVANCED_OPTS_READ_PROCESSING@">
         #if $advancedOpt.doExtendCustom.doExtend == 'custom':
             --extendReads $advancedOpt.doExtendCustom.extendReadsValue
diff --git a/galaxy/wrapper/plotCoverage.xml b/galaxy/wrapper/plotCoverage.xml
index 6cc46b632..ef17add13 100644
--- a/galaxy/wrapper/plotCoverage.xml
+++ b/galaxy/wrapper/plotCoverage.xml
@@ -38,6 +38,7 @@
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
                 @ADVANCED_OPTS_READ_PROCESSING@
+                @PLOTWIDTHHEIGHT@
                 @blacklist@
             #end if
 
@@ -57,6 +58,7 @@
                 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                    label="Number of samples"
                    help="Number of samples taken from the genome to compute the scaling factors."/>
+                <expand macro="plotWidthHeight" width="15" height="5" />
                 <expand macro="region_limit_operation" />
                 <expand macro="read_processing_options" />
                 <expand macro="skipZeros" />