From f3e91d1490bf5045acefe8ab366d27ca115a72a9 Mon Sep 17 00:00:00 2001
From: niekwit <41302859+niekwit@users.noreply.github.com>
Date: Thu, 21 May 2026 10:10:04 +0100
Subject: [PATCH] plotHeatmap: add --plotColors argument for profile plot line
 colors

Allows users to set custom colors for the profile/summary plot lines
when --whatToShow includes a plot. Colors are recycled if fewer are
given than the number of lines. Accepts any matplotlib named color
or hex value. Consistent with the existing --colorList approach.
---
 deeptools/parserCommon.py | 21 +++++++++++++++++++++
 deeptools/plotHeatmap.py  | 26 +++++++++++++++++++-------
 2 files changed, 40 insertions(+), 7 deletions(-)

diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py
index 9849d9c431..e8798c9228 100755
--- a/deeptools/parserCommon.py
+++ b/deeptools/parserCommon.py
@@ -2,6 +2,7 @@
 import os
 from importlib.metadata import version
 import multiprocessing
+import matplotlib.colors
 
 
 def check_float_0_1(value):
@@ -22,6 +23,15 @@ def check_list_of_comma_values(value):
     return value
 
 
+def check_color(value):
+    """Validate that a string is a recognised matplotlib color (named or hex)."""
+    if not matplotlib.colors.is_color_like(value):
+        raise argparse.ArgumentTypeError(
+            "'{}' is not a valid matplotlib color. Use a named color "
+            "(e.g. 'red') or a hex value (e.g. '#ff0000').".format(value))
+    return value
+
+
 def output(args=None):
     parser = argparse.ArgumentParser(add_help=False)
     group = parser.add_argument_group('Output')
@@ -704,6 +714,17 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
             type=int,
             default=256)
 
+        optional.add_argument(
+            '--plotColors',
+            help='Colors for the profile lines in the summary plot shown above the heatmap. '
+                 'Only applies when --whatToShow is set to "plot, heatmap and colorbar" or '
+                 '"plot and heatmap". One color per group (or per sample when --perGroup is set) '
+                 'can be specified. Colors are recycled if fewer are given than the number of lines. '
+                 'Accepts named matplotlib colors (e.g. red, blue) and hex values (e.g. #ff0000). '
+                 'Example: --plotColors red blue green',
+            type=check_color,
+            nargs='+')
+
         optional.add_argument('--zMin', '-min',
                               default=None,
                               help='Minimum value for the heatmap intensities. Multiple values, separated by '
diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index a2149f8299..359bc303f6 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -379,7 +379,7 @@ def plotlyMatrix(hm,
 
 
 def plotMatrix(hm, outFileName,
-               colorMapDict={'colorMap': ['binary'], 'missingDataColor': 'black', 'alpha': 1.0},
+               colorMapDict={'colorMap': ['binary'], 'missingDataColor': 'black', 'alpha': 1.0, 'plotColors': None},
                plotTitle='',
                xAxisLabel='', yAxisLabel='', regionsLabel='',
                zMin=None, zMax=None,
@@ -531,13 +531,24 @@ def plotMatrix(hm, outFileName,
         fig
     )
 
-    # color map for the summary plot (profile) on top of the heatmap
-    cmap_plot = plt.get_cmap('jet')
+    # colors for the profile lines in the summary plot above the heatmap
     numgroups = hm.matrix.get_num_groups()
-    if perGroup:
-        color_list = cmap_plot(np.arange(hm.matrix.get_num_samples()) / hm.matrix.get_num_samples())
+    if colorMapDict.get('plotColors'):
+        # user-supplied colors: one per group (or per sample when perGroup),
+        # recycled with modulo if fewer colors are given than lines
+        user_colors = colorMapDict['plotColors']
+        if perGroup:
+            n_lines = hm.matrix.get_num_samples()
+        else:
+            n_lines = numgroups
+        color_list = [user_colors[i % len(user_colors)] for i in range(n_lines)]
     else:
-        color_list = cmap_plot(np.arange(numgroups) / numgroups)
+        # default: evenly-spaced colors from the jet colormap
+        cmap_plot = plt.get_cmap('jet')
+        if perGroup:
+            color_list = cmap_plot(np.arange(hm.matrix.get_num_samples()) / hm.matrix.get_num_samples())
+        else:
+            color_list = cmap_plot(np.arange(numgroups) / numgroups)
     alpha = colorMapDict['alpha']
     if image_format == 'plotly':
         return plotlyMatrix(hm,
@@ -867,7 +878,8 @@ def main(args=None):
                      'colorList': args.colorList,
                      'colorNumber': args.colorNumber,
                      'missingDataColor': args.missingDataColor,
-                     'alpha': args.alpha}
+                     'alpha': args.alpha,
+                     'plotColors': args.plotColors}
 
     plotMatrix(hm,
                args.outFileName,