deeptools · LeilyR · Aug 10, 2020 · Jul 10, 2020 · Jul 10, 2020 · Jul 23, 2020
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,12 @@
+3.5.0
+
+ * Fixed a small issue in computeGCBias (issue #969)
+ * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile.
+ * Fixed a small typo in bamCompare. (issue #966)
+ * Save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again.(issue #953)
+ * Different colors can now be set by user for plotProfile --plotType heatmap (issue #956)
+ * `auto` option now has been added to the zMin and zMax of plotHeatmap. (issue #908)
+
 3.4.3
 
  * Changed iteritems() in estimateEscaleFactor to its python3 compatible items().

diff --git a/deeptools/_version.py b/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__ = '3.4.3'
+__version__ = '3.5.0'
diff --git a/deeptools/computeGCBias.py b/deeptools/computeGCBias.py
@@ -604,7 +604,7 @@ def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_format=N
     plt.setp(bp['whiskers'], color='black', linestyle='dashed')
     plt.setp(bp['fliers'], marker='None')
     # get the whisker that spands the most
-    y_max = max([x.get_data()[1][1] for x in bp['whiskers']])
+    y_max = np.nanmax([x.get_data()[1][1] for x in bp['whiskers']])
     ax1.set_ylim(0 - (y_max * 0.05), y_max * 1.05)
     ax1.set_ylabel('Number of reads')
     ax1.set_xlabel('GC fraction')

diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py
@@ -361,8 +361,7 @@ def numberOfProcessors(string):
             raise argparse.ArgumentTypeError("the given value {} is not valid. "
                                              "Error message: {}\nThe number of "
                                              "available processors in your "
-                                             "computer is {}.".format(string, e,
-                                                                      availProc))
+                                             "computer is {}.".format(string, e, availProc))
 
         if numberOfProcessors > availProc:
             numberOfProcessors = availProc
@@ -704,15 +703,17 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
                               default=None,
                               help='Minimum value for the heatmap intensities. Multiple values, separated by '
                                    'spaces can be set for each heatmap. If the number of zMin values is smaller than'
-                                   'the number of heatmaps the values are recycled.',
-                              type=float,
+                                   'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '
+                                   ' to the first percentile of the matrix values.',
+                              type=str,
                               nargs='+')
         optional.add_argument('--zMax', '-max',
                               default=None,
                               help='Maximum value for the heatmap intensities. Multiple values, separated by '
                                    'spaces can be set for each heatmap. If the number of zMax values is smaller than'
-                                   'the number of heatmaps the values are recycled.',
-                              type=float,
+                                   'the number of heatmaps the values are recycled. If a value is set to "auto", it will be set '
+                                   ' to the 98th percentile of the matrix values.',
+                              type=str,
                               nargs='+')
         optional.add_argument('--heatmapHeight',
                               help='Plot height in cm. The default for the heatmap '

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
@@ -412,6 +412,16 @@ def plotMatrix(hm, outFileName,
             zMin = [None]
         else:
             zMin = [zMin]  # convert to list to support multiple entries
+    elif 'auto' in zMin:
+        matrix_flatten = hm.matrix.flatten()
+        auto_min = np.percentile(matrix_flatten, 1.0)
+        if np.isnan(auto_min):
+            auto_min = None
+        new_mins = [float(x) if x != 'auto' else auto_min for x in zMin]
+        zMin = new_mins
+    else:
+        new_mins = [float(x) for x in zMin]
+        zMin = new_mins
 
     if zMax is None:
         if matrix_flatten is None:
@@ -422,6 +432,23 @@ def plotMatrix(hm, outFileName,
             zMax = [None]
         else:
             zMax = [zMax]
+    elif 'auto' in zMax:
+        matrix_flatten = hm.matrix.flatten()
+        auto_max = np.percentile(matrix_flatten, 98.0)
+        if np.isnan(auto_max):
+            auto_max = None
+        new_maxs = [float(x) if x != 'auto' else auto_max for x in zMax]
+        zMax = new_maxs
+    else:
+        new_maxs = [float(x) for x in zMax]
+        zMax = new_maxs
+    if (len(zMin) > 1) & (len(zMax) > 1):
+        for index, value in enumerate(zMax):
+            if value <= zMin[index]:
+                sys.stderr.write("Warnirng: In bigwig {}, the given zmin ({}) is larger than "
+                                 "or equal to the given zmax ({}). Thus, it has been set "
+                                 "to None. \n".format(index + 1, zMin[index], value))
+                zMin[index] = None
 
     if yMin is None:
         yMin = [None]

diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.4.3.0</token>
+    <token name="@WRAPPER_VERSION@">3.5.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.4.3">deeptools</requirement>
+            <requirement type="package" version="3.5.0">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />