From db8e849befbec8f91d047f0f7dcfa2d8d9ec5243 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Tue, 29 Jun 2021 19:06:41 -0500
Subject: [PATCH 01/11] move legend to up and fix y-axis inward if using
 different ymax

---
 deeptools/plotHeatmap.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index bc4bbcc2a4..cbf2ddb62d 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -161,6 +161,7 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
         if sample_id > 0 and len(yMin) == 1 and len(yMax) == 1:
             plt.setp(ax_profile.get_yticklabels(), visible=False)
 
+        ax_profile.get_yaxis().set_tick_params(direction='in',pad=-22) # beisi
         if sample_id == 0 and yAxisLabel != '':
             ax_profile.set_ylabel(yAxisLabel)
         xticks, xtickslabel = hm.getTicks(tickIdx)
@@ -593,8 +594,13 @@ def plotMatrix(hm, outFileName,
             ax_list = addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType, plot_type, yAxisLabel, color_list, yMin, yMax, kwargs['wspace'], kwargs['hspace'], colorbar_position, label_rotation)
 
         if legend_location != 'none':
-            ax_list[-1].legend(loc=legend_location.replace('-', ' '), ncol=1, prop=fontP,
-                               frameon=False, markerscale=0.5)
+            ax = ax_list[-1] # beisi
+            box = ax.get_position()
+            ax.set_position([box.x0, box.y0 - box.height * 0.1, box.width, box.height * 0.9])
+            legend = ax.legend(loc='lower right', shadow=False, fontsize='x-large', bbox_to_anchor=(0, 1.3, 1, .22), ncol=10, frameon=False, prop=fontP) # beisi, legend line
+            ax.add_artist(legend)
+            #            ax_list[-1].legend(loc=legend_location.replace('-', ' '), ncol=1, prop=fontP,
+            #                   frameon=False, markerscale=0.5)
 
     first_group = 0  # helper variable to place the title per sample/group
     for sample in range(hm.matrix.get_num_samples()):

From 30f42e99b8fa073e14047b4de3f83aa975142c61 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Tue, 11 Jul 2023 18:43:25 -0500
Subject: [PATCH 02/11] autobreakline for title and rotation y label of heatmap

---
 deeptools/heatmapper.py  |  4 ++--
 deeptools/plotHeatmap.py | 19 ++++++++++++++-----
 deeptools/plotProfile.py | 15 ++++++++++++---
 3 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/deeptools/heatmapper.py b/deeptools/heatmapper.py
index 6a95ba0052..d0eebaad22 100644
--- a/deeptools/heatmapper.py
+++ b/deeptools/heatmapper.py
@@ -1308,9 +1308,9 @@ def hmcluster(self, k, evaluate_silhouette=True, method='kmeans', clustering_sam
         _clustered_matrix = []
         cluster_number = 1
         for cluster in cluster_order:
-            self.group_labels.append("cluster_{}".format(cluster_number))
-            cluster_number += 1
             cluster_ids = _cluster_ids_list[cluster]
+            self.group_labels.append("cluster_{}_n{}".format(cluster_number,len(cluster_ids)))
+            cluster_number += 1
             self.group_boundaries.append(self.group_boundaries[-1] +
                                          len(cluster_ids))
             _clustered_matrix.append(self.matrix[cluster_ids, :])
diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index cbf2ddb62d..521ebc388e 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -13,7 +13,7 @@
 from matplotlib.font_manager import FontProperties
 import matplotlib.gridspec as gridspec
 from matplotlib import ticker
-import copy
+import copy, re
 import sys
 import plotly.offline as py
 import plotly.graph_objs as go
@@ -115,6 +115,15 @@ def prepare_layout(hm_matrix, heatmapsize, showSummaryPlot, showColorbar, perGro
 
     return grids
 
+def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
+    sss = [ rr for rr in re.split(sep,title) if len(rr) ]
+    newtitle, tmp = "", ""
+    for ss in sss:
+        tmp += ss
+        if len(tmp) > lmax:
+            newtitle += tmp + "\n"
+            tmp = ""
+    return newtitle
 
 def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType, plot_type, yAxisLabel, color_list, yMin, yMax, wspace, hspace, colorbar_position, label_rotation=0.0):
     """
@@ -144,7 +153,7 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
             else:
                 ax_profile = fig.add_subplot(grids[0, sample_id])
 
-        ax_profile.set_title(title)
+        ax_profile.set_title(autobreaklinetitle(title))
         for group in range(iterNum2):
             if perGroup:
                 sub_matrix = hm.matrix.get_matrix(sample_id, group)
@@ -636,7 +645,7 @@ def plotMatrix(hm, outFileName,
 
             if group == first_group and not showSummaryPlot and not perGroup:
                 title = hm.matrix.sample_labels[sample]
-                ax.set_title(title)
+                ax_profile.set_title(autobreaklinetitle(title))
 
             if box_around_heatmaps is False:
                 # Turn off the boxes around the individual heatmaps
@@ -689,9 +698,9 @@ def plotMatrix(hm, outFileName,
                 ax.axes.set_xlabel(xAxisLabel)
             ax.axes.set_yticks([])
             if perGroup and group == 0:
-                ax.axes.set_ylabel(sub_matrix['sample'])
+                ax.axes.set_ylabel(sub_matrix['sample'],rotation=75,labelpad=0,fontsize=15)
             elif not perGroup and sample == 0:
-                ax.axes.set_ylabel(sub_matrix['group'])
+                ax.axes.set_ylabel(sub_matrix['group'],rotation=75,labelpad=0,horizontalalignment='right',fontsize=15)
 
             # Plot vertical lines at tick marks if desired
             if linesAtTickMarks:
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index b46be32bb9..aa8afc30a8 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -49,6 +49,15 @@ def parse_arguments(args=None):
 
     return parser
 
+def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
+    sss = [ rr for rr in re.split(sep,title) if len(rr) ]
+    newtitle, tmp = "", ""
+    for ss in sss:
+        tmp += ss
+        if len(tmp) > lmax:
+            newtitle += tmp + "\n"
+            tmp = ""
+    return newtitle
 
 def process_args(args=None):
     args = parse_arguments().parse_args(args)
@@ -269,7 +278,7 @@ def plot_hexbin(self):
             for data_idx in range(self.numlines)[::-1]:
                 ax = self.fig.add_subplot(sub_grid[data_idx, 0])
                 if data_idx == 0:
-                    ax.set_title(title)
+                    ax.set_title(autobreaklinetitle(title))
                 if data_idx != self.numlines - 1:
                     plt.setp(ax.get_xticklabels(), visible=False)
 
@@ -514,7 +523,7 @@ def plot_heatmap(self):
             else:
                 title = self.hm.matrix.sample_labels[plot]
                 tickIdx = plot
-            ax.set_title(title)
+            ax.set_title(autobreaklinetitle(title))
             mat = []  # when drawing a heatmap (in contrast to drawing lines)
             for data_idx in range(self.numlines):
                 if self.per_group:
@@ -723,7 +732,7 @@ def plot_profile(self):
                     plt.setp(ax.get_yticklabels(), visible=False)
                 tickIdx = plot
 
-            ax.set_title(title)
+            ax.set_title(autobreaklinetitle(title))
             for data_idx in range(self.numlines):
                 if self.per_group:
                     _row, _col = plot, data_idx

From f1481a4cbe09404f02e44bb2d7d725502bc50493 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Tue, 11 Jul 2023 18:44:27 -0500
Subject: [PATCH 03/11] autobreakline for title and rotation y label of heatmap

---
 deeptools/plotHeatmap.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index 521ebc388e..7285ea816a 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -645,7 +645,7 @@ def plotMatrix(hm, outFileName,
 
             if group == first_group and not showSummaryPlot and not perGroup:
                 title = hm.matrix.sample_labels[sample]
-                ax_profile.set_title(autobreaklinetitle(title))
+                ax.set_title(autobreaklinetitle(title))
 
             if box_around_heatmaps is False:
                 # Turn off the boxes around the individual heatmaps

From 7cacf3cb5243f9a46d085367c2629e9397eeaebb Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 12 Jul 2023 10:53:08 -0500
Subject: [PATCH 04/11] debug title

---
 deeptools/plotHeatmap.py | 2 ++
 deeptools/plotProfile.py | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index 7285ea816a..e7657172a2 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -123,6 +123,8 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
         if len(tmp) > lmax:
             newtitle += tmp + "\n"
             tmp = ""
+        else:
+            tmp += "-"
     return newtitle
 
 def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType, plot_type, yAxisLabel, color_list, yMin, yMax, wspace, hspace, colorbar_position, label_rotation=0.0):
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index aa8afc30a8..5011234c1a 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -57,6 +57,8 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
         if len(tmp) > lmax:
             newtitle += tmp + "\n"
             tmp = ""
+        else:
+            tmp += "-"
     return newtitle
 
 def process_args(args=None):

From a7059c1b3916482db341e41161e869d610a67bef Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 12 Jul 2023 15:07:46 -0500
Subject: [PATCH 05/11] debug title

---
 deeptools/plotHeatmap.py | 1 +
 deeptools/plotProfile.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index e7657172a2..0358390984 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -125,6 +125,7 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
             tmp = ""
         else:
             tmp += "-"
+    newtitle += tmp.strip("-") + "\n"
     return newtitle
 
 def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType, plot_type, yAxisLabel, color_list, yMin, yMax, wspace, hspace, colorbar_position, label_rotation=0.0):
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index 5011234c1a..ce49e82ab5 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -59,6 +59,7 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
             tmp = ""
         else:
             tmp += "-"
+    newtitle += tmp.strip("-") + "\n"
     return newtitle
 
 def process_args(args=None):

From 23c5e1601c909cdab9b744af2b7d225818a3f9c5 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 12 Jul 2023 16:20:58 -0500
Subject: [PATCH 06/11] small tweak

---
 deeptools/plotHeatmap.py | 3 ++-
 deeptools/plotProfile.py | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index 0358390984..688d41df1d 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -125,7 +125,8 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
             tmp = ""
         else:
             tmp += "-"
-    newtitle += tmp.strip("-") + "\n"
+    newtitle += tmp.strip("-")
+    newtitle = "\n" + newtitle
     return newtitle
 
 def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType, plot_type, yAxisLabel, color_list, yMin, yMax, wspace, hspace, colorbar_position, label_rotation=0.0):
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index ce49e82ab5..f100a9eac8 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 
-import sys
+import sys, re
 
 import argparse
 import numpy as np
@@ -59,7 +59,8 @@ def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
             tmp = ""
         else:
             tmp += "-"
-    newtitle += tmp.strip("-") + "\n"
+    newtitle += tmp.strip("-")
+    newtitle = "\n" + newtitle
     return newtitle
 
 def process_args(args=None):

From 1b85c00c8c0efa1b10f724ff4ae338aec651e5d1 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Mon, 2 Oct 2023 18:09:32 -0500
Subject: [PATCH 07/11] hard limit to 15 chars

---
 deeptools/plotHeatmap.py | 16 +++++++++-------
 deeptools/plotProfile.py | 14 ++++++++------
 2 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
index 688d41df1d..d2f8b5a18c 100755
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -13,8 +13,8 @@
 from matplotlib.font_manager import FontProperties
 import matplotlib.gridspec as gridspec
 from matplotlib import ticker
-import copy, re
-import sys
+
+import sys, re, os, copy
 import plotly.offline as py
 import plotly.graph_objs as go
 
@@ -115,17 +115,19 @@ def prepare_layout(hm_matrix, heatmapsize, showSummaryPlot, showColorbar, perGro
 
     return grids
 
-def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
+def autobreaklinetitle(title,sep="[-_,.:]",lmax=15):
+    outsep = "-"
     sss = [ rr for rr in re.split(sep,title) if len(rr) ]
     newtitle, tmp = "", ""
     for ss in sss:
+        tmp0 = tmp
         tmp += ss
         if len(tmp) > lmax:
-            newtitle += tmp + "\n"
-            tmp = ""
+            newtitle += tmp0.strip(outsep) + "\n"
+            tmp = ss
         else:
-            tmp += "-"
-    newtitle += tmp.strip("-")
+            tmp += outsep
+    newtitle += tmp.strip(outsep)
     newtitle = "\n" + newtitle
     return newtitle
 
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index f100a9eac8..6655d5940d 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 
-import sys, re
+import sys, os, re
 
 import argparse
 import numpy as np
@@ -49,17 +49,19 @@ def parse_arguments(args=None):
 
     return parser
 
-def autobreaklinetitle(title,sep="[-_,.]",lmax=15):
+def autobreaklinetitle(title,sep="[-_,.:]",lmax=15):
+    outsep = "-"
     sss = [ rr for rr in re.split(sep,title) if len(rr) ]
     newtitle, tmp = "", ""
     for ss in sss:
+        tmp0 = tmp
         tmp += ss
         if len(tmp) > lmax:
-            newtitle += tmp + "\n"
-            tmp = ""
+            newtitle += tmp0.strip(outsep) + "\n"
+            tmp = ss
         else:
-            tmp += "-"
-    newtitle += tmp.strip("-")
+            tmp += outsep
+    newtitle += tmp.strip(outsep)
     newtitle = "\n" + newtitle
     return newtitle
 

From e793e4840e500c811cf4258e407bd60e76d5d359 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 22 Nov 2023 13:01:56 -0600
Subject: [PATCH 08/11] add --repgrplist option to combine replicates for
 plotProfile

---
 deeptools/heatmapper_utilities.py |  21 +++++-
 deeptools/parserCommon.py         |   8 +++
 deeptools/plotProfile.py          | 109 +++++++++++++++++++++---------
 3 files changed, 103 insertions(+), 35 deletions(-)

diff --git a/deeptools/heatmapper_utilities.py b/deeptools/heatmapper_utilities.py
index e63dfb0226..aa3559096f 100644
--- a/deeptools/heatmapper_utilities.py
+++ b/deeptools/heatmapper_utilities.py
@@ -9,6 +9,9 @@
 
 old_settings = np.seterr(all='ignore')
 
+debug = 0
+if debug:
+    from ipdb import set_trace
 
 def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
     """
@@ -18,7 +21,7 @@ def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
     ----------
     ax : matplotlib axis
         matplotlib axis
-    ma : numpy array
+    ma : numpy array or list of numpy array(for plot with --repgrplist, take average between replicates )
         numpy array The data on this matrix is summarized according
         to the `average_type` argument.
     average_type : str
@@ -32,7 +35,9 @@ def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
         type of plot. Either 'se' for standard error, 'std' for
         standard deviation, 'overlapped_lines' to plot each line of the matrix,
         fill to plot the area between the x axis and the value or any other string to
-        just plot the average line.
+        just plot the average line. When assign samples to replicates group such as
+        '--repgrplist WT WT KO KO' : 'std' would be the standard deviation between replicates groups.
+        'se' for standard error between replicates groups.
 
     Returns
     -------
@@ -63,7 +68,15 @@ def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
 
 
     """
-    summary = np.ma.__getattribute__(average_type)(ma, axis=0)
+    if isinstance(ma,list):
+        summary_list = []
+        for ma_each in ma:
+            tmp = np.ma.__getattribute__(average_type)(ma_each, axis=0)
+            summary_list.append(tmp)
+        ma = np.array(summary_list)
+        summary = np.ma.__getattribute__("average")(ma, axis=0)
+    else:
+        summary = np.ma.__getattribute__(average_type)(ma, axis=0)
     # only plot the average profiles without error regions
     x = np.arange(len(summary))
     if isinstance(color, np.ndarray):
@@ -72,6 +85,8 @@ def plot_single(ax, ma, average_type, color, label, plot_type='lines'):
     if plot_type == 'fill':
         ax.fill_between(x, summary, facecolor=color, alpha=0.6, edgecolor='none')
 
+    if debug:
+        set_trace()
     if plot_type in ['se', 'std']:
         if plot_type == 'se':  # standard error
             std = np.std(ma, axis=0) / np.sqrt(ma.shape[0])
diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py
index ef4f4d0748..23de9e6472 100755
--- a/deeptools/parserCommon.py
+++ b/deeptools/parserCommon.py
@@ -846,6 +846,14 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
                           'group.',
                           action='store_true')
 
+    optional.add_argument('--repgrplist',
+                          default=None,
+                          nargs='+',
+                          help='Group profiles by genotype'
+                               'assign each profile to a group(as replicates) to plot average +/- se/std.'
+                               'If the number of group values is smaller than'
+                               'the number of plots, the values are recycled.')
+
     optional.add_argument('--plotFileFormat',
                           metavar='',
                           help='Image format type. If given, this '
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index 6655d5940d..8df0bf679d 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -26,12 +26,12 @@
 from deeptools.heatmapper_utilities import plot_single, plotly_single, getProfileTicks
 from deeptools.computeMatrixOperations import filterHeatmapValues
 
-
 debug = 0
+if debug:
+    from ipdb import set_trace
 old_settings = np.seterr(all='ignore')
 plt.ioff()
 
-
 def parse_arguments(args=None):
     parser = argparse.ArgumentParser(
         parents=[parserCommon.heatmapperMatrixArgs(),
@@ -111,6 +111,7 @@ def __init__(self, hm, out_file_name,
                  plot_height=7,
                  plot_width=11,
                  per_group=False,
+                 repgrplist=None,
                  plot_type='lines',
                  image_format=None,
                  color_list=None,
@@ -137,6 +138,7 @@ def __init__(self, hm, out_file_name,
             plot_height: in cm
             plot_width: in cm
             per_group: bool
+            repgrplist: list
             plot_type: string
             image_format: string
             color_list: list
@@ -160,6 +162,7 @@ def __init__(self, hm, out_file_name,
         self.plot_height = plot_height
         self.plot_width = plot_width
         self.per_group = per_group
+        self.repgrplist = repgrplist
         self.plot_type = plot_type
         self.image_format = image_format
         self.color_list = color_list
@@ -171,11 +174,13 @@ def __init__(self, hm, out_file_name,
         # Honor reference point labels from computeMatrix
         if reference_point_label is None:
             self.reference_point_label = hm.parameters['ref point']
-
         # decide how many plots are needed
         if self.per_group:
             self.numplots = self.hm.matrix.get_num_groups()
-            self.numlines = self.hm.matrix.get_num_samples()
+            if self.repgrplist:
+                self.numlines = len(set(self.repgrplist))
+            else:
+                self.numlines = self.hm.matrix.get_num_samples()
         else:
             self.numplots = self.hm.matrix.get_num_samples()
             self.numlines = self.hm.matrix.get_num_groups()
@@ -525,7 +530,7 @@ def plot_heatmap(self):
 
             if self.per_group:
                 title = self.hm.matrix.group_labels[plot]
-                tickIdx = plot % self.hm.matrix.get_num_samples()
+                tickIdx = plot % self.numlines
             else:
                 title = self.hm.matrix.sample_labels[plot]
                 tickIdx = plot
@@ -731,7 +736,7 @@ def plot_profile(self):
                 title = self.hm.matrix.group_labels[plot]
                 if row != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
                     plt.setp(ax.get_yticklabels(), visible=False)
-                tickIdx = plot % self.hm.matrix.get_num_samples()
+                tickIdx = plot % self.numlines
             else:
                 title = self.hm.matrix.sample_labels[plot]
                 if col != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
@@ -739,32 +744,71 @@ def plot_profile(self):
                 tickIdx = plot
 
             ax.set_title(autobreaklinetitle(title))
-            for data_idx in range(self.numlines):
-                if self.per_group:
-                    _row, _col = plot, data_idx
-                else:
-                    _row, _col = data_idx, plot
-                if localYMin is None or self.y_min[col % len(self.y_min)] < localYMin:
-                    localYMin = self.y_min[col % len(self.y_min)]
-                if localYMax is None or self.y_max[col % len(self.y_max)] > localYMax:
-                    localYMax = self.y_max[col % len(self.y_max)]
-
-                sub_matrix = self.hm.matrix.get_matrix(_row, _col)
-
-                if self.per_group:
-                    label = sub_matrix['sample']
-                else:
-                    label = sub_matrix['group']
-
-                if self.numlines > 1:
-                    coloridx = data_idx
-                else:
-                    coloridx = plot
-                plot_single(ax, sub_matrix['matrix'],
-                            self.averagetype,
-                            self.color_list[coloridx],
-                            label,
-                            plot_type=self.plot_type)
+            if localYMin is None or self.y_min[col % len(self.y_min)] < localYMin:
+                localYMin = self.y_min[col % len(self.y_min)]
+            if localYMax is None or self.y_max[col % len(self.y_max)] > localYMax:
+                localYMax = self.y_max[col % len(self.y_max)]
+            if self.per_group and self.repgrplist:
+                nsamptmp = self.hm.matrix.get_num_samples()
+                repgrplistuniq = []
+                repgrp_samp_dict = {}
+                for tmp in self.repgrplist:
+                    if not tmp in repgrplistuniq:
+                        repgrplistuniq.append(tmp)
+                for data_idx in range(nsamptmp):
+                    thisrepgrp = repgrplistuniq[int(data_idx / (nsamptmp/self.numlines))]
+                    try:
+                        repgrp_samp_dict[thisrepgrp].append(data_idx)
+                    except:
+                        repgrp_samp_dict[thisrepgrp] = [ data_idx ]
+                
+                for irepgrp, repgrp in enumerate(repgrplistuniq):
+                    sub_matrix_list = []
+                    for data_idx in repgrp_samp_dict[repgrp]:
+                        _row, _col = plot, data_idx
+                        sub_matrix = self.hm.matrix.get_matrix(_row, _col)
+                        sub_matrix_list.append(sub_matrix['matrix'])
+                    if debug:
+                        set_trace()
+    
+                    label = f"{repgrp}(n={len(repgrp_samp_dict[repgrp])})"
+    
+                    if self.numlines > 1:
+                        coloridx = irepgrp
+                    else:
+                        coloridx = plot
+                    plot_single(ax, sub_matrix_list,
+                                self.averagetype,
+                                self.color_list[coloridx],
+                                label,
+                                plot_type=self.plot_type)
+            else:
+                for data_idx in range(self.numlines):
+                    if self.per_group:
+                        _row, _col = plot, data_idx
+                    else:
+                        _row, _col = data_idx, plot
+                    if localYMin is None or self.y_min[col % len(self.y_min)] < localYMin:
+                        localYMin = self.y_min[col % len(self.y_min)]
+                    if localYMax is None or self.y_max[col % len(self.y_max)] > localYMax:
+                        localYMax = self.y_max[col % len(self.y_max)]
+    
+                    sub_matrix = self.hm.matrix.get_matrix(_row, _col)
+    
+                    if self.per_group:
+                        label = sub_matrix['sample']
+                    else:
+                        label = sub_matrix['group']
+    
+                    if self.numlines > 1:
+                        coloridx = data_idx
+                    else:
+                        coloridx = plot
+                    plot_single(ax, sub_matrix['matrix'],
+                                self.averagetype,
+                                self.color_list[coloridx],
+                                label,
+                                plot_type=self.plot_type)
             globalYmin = min(np.float64(globalYmin), ax.get_ylim()[0])
             globalYmax = max(globalYmax, ax.get_ylim()[1])
 
@@ -970,6 +1014,7 @@ def main(args=None):
                    plot_height=args.plotHeight,
                    plot_width=args.plotWidth,
                    per_group=args.perGroup,
+                   repgrplist=args.repgrplist,
                    plot_type=args.plotType,
                    image_format=args.plotFileFormat,
                    color_list=args.colors,

From f05c5faf8eaebf1f45d9cf1517d133f2150e04c7 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 22 Nov 2023 14:39:06 -0600
Subject: [PATCH 09/11] debug --repgrplist if number matching number of samples

---
 deeptools/parserCommon.py |  2 +-
 deeptools/plotProfile.py  | 28 ++++++++++++++++++----------
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/deeptools/parserCommon.py b/deeptools/parserCommon.py
index 23de9e6472..ce11b399f5 100755
--- a/deeptools/parserCommon.py
+++ b/deeptools/parserCommon.py
@@ -852,7 +852,7 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
                           help='Group profiles by genotype'
                                'assign each profile to a group(as replicates) to plot average +/- se/std.'
                                'If the number of group values is smaller than'
-                               'the number of plots, the values are recycled.')
+                               'the number of samples, the values will be equally divide into groups.')
 
     optional.add_argument('--plotFileFormat',
                           metavar='',
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index 8df0bf679d..69b536b37a 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -750,17 +750,25 @@ def plot_profile(self):
                 localYMax = self.y_max[col % len(self.y_max)]
             if self.per_group and self.repgrplist:
                 nsamptmp = self.hm.matrix.get_num_samples()
-                repgrplistuniq = []
                 repgrp_samp_dict = {}
-                for tmp in self.repgrplist:
-                    if not tmp in repgrplistuniq:
-                        repgrplistuniq.append(tmp)
-                for data_idx in range(nsamptmp):
-                    thisrepgrp = repgrplistuniq[int(data_idx / (nsamptmp/self.numlines))]
-                    try:
-                        repgrp_samp_dict[thisrepgrp].append(data_idx)
-                    except:
-                        repgrp_samp_dict[thisrepgrp] = [ data_idx ]
+                if len(self.repgrplist) == nsamptmp:
+                    for data_idx in range(nsamptmp):
+                        thisrepgrp = self.repgrplist[data_idx]
+                        try:
+                            repgrp_samp_dict[thisrepgrp].append(data_idx)
+                        except:
+                            repgrp_samp_dict[thisrepgrp] = [ data_idx ]
+                else:
+                    repgrplistuniq = []
+                    for tmp in self.repgrplist:
+                        if not tmp in repgrplistuniq:
+                            repgrplistuniq.append(tmp)
+                    for data_idx in range(nsamptmp):
+                        thisrepgrp = repgrplistuniq[int(data_idx / (nsamptmp/self.numlines))]
+                        try:
+                            repgrp_samp_dict[thisrepgrp].append(data_idx)
+                        except:
+                            repgrp_samp_dict[thisrepgrp] = [ data_idx ]
                 
                 for irepgrp, repgrp in enumerate(repgrplistuniq):
                     sub_matrix_list = []

From 01caa598f8125541d3a4d06b48a9f08387414553 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 22 Nov 2023 14:45:20 -0600
Subject: [PATCH 10/11] debug --repgrplist if number matching number of samples

---
 deeptools/plotProfile.py | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index 69b536b37a..7bf4c61b78 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -751,24 +751,20 @@ def plot_profile(self):
             if self.per_group and self.repgrplist:
                 nsamptmp = self.hm.matrix.get_num_samples()
                 repgrp_samp_dict = {}
-                if len(self.repgrplist) == nsamptmp:
-                    for data_idx in range(nsamptmp):
+                repgrplistuniq = []
+                for tmp in self.repgrplist:
+                    if not tmp in repgrplistuniq:
+                        repgrplistuniq.append(tmp)
+
+                for data_idx in range(nsamptmp):
+                    if len(self.repgrplist) >= nsamptmp:
                         thisrepgrp = self.repgrplist[data_idx]
-                        try:
-                            repgrp_samp_dict[thisrepgrp].append(data_idx)
-                        except:
-                            repgrp_samp_dict[thisrepgrp] = [ data_idx ]
-                else:
-                    repgrplistuniq = []
-                    for tmp in self.repgrplist:
-                        if not tmp in repgrplistuniq:
-                            repgrplistuniq.append(tmp)
-                    for data_idx in range(nsamptmp):
+                    else:
                         thisrepgrp = repgrplistuniq[int(data_idx / (nsamptmp/self.numlines))]
-                        try:
-                            repgrp_samp_dict[thisrepgrp].append(data_idx)
-                        except:
-                            repgrp_samp_dict[thisrepgrp] = [ data_idx ]
+                    try:
+                        repgrp_samp_dict[thisrepgrp].append(data_idx)
+                    except:
+                        repgrp_samp_dict[thisrepgrp] = [ data_idx ]
                 
                 for irepgrp, repgrp in enumerate(repgrplistuniq):
                     sub_matrix_list = []

From 4e19dcbb4c79be497c306be928280165c74101f3 Mon Sep 17 00:00:00 2001
From: "Xu, Beisi" <Beisi.Xu@STJUDE.ORG>
Date: Wed, 22 Nov 2023 14:52:38 -0600
Subject: [PATCH 11/11] debug --repgrplist if number matching number of samples

---
 deeptools/plotProfile.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index 7bf4c61b78..dddea44482 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -766,14 +766,14 @@ def plot_profile(self):
                     except:
                         repgrp_samp_dict[thisrepgrp] = [ data_idx ]
                 
+                if debug:
+                    set_trace()
                 for irepgrp, repgrp in enumerate(repgrplistuniq):
                     sub_matrix_list = []
                     for data_idx in repgrp_samp_dict[repgrp]:
                         _row, _col = plot, data_idx
                         sub_matrix = self.hm.matrix.get_matrix(_row, _col)
                         sub_matrix_list.append(sub_matrix['matrix'])
-                    if debug:
-                        set_trace()
     
                     label = f"{repgrp}(n={len(repgrp_samp_dict[repgrp])})"