From 2b1fde0022944d641d8b31f6384e58feb72705e0 Mon Sep 17 00:00:00 2001
From: mnshgl0110 <mnshgl0110@gmail.com>
Date: Thu, 23 Nov 2023 16:02:07 +0100
Subject: [PATCH] bugfix: https://github.com/schneebergerlab/plotsr/issues/72

---
 plotsr/__init__.py     |  2 +-
 plotsr/scripts/func.py | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/plotsr/__init__.py b/plotsr/__init__.py
index 72f26f5..0b2f79d 100755
--- a/plotsr/__init__.py
+++ b/plotsr/__init__.py
@@ -1 +1 @@
-__version__ = "1.1.2"
+__version__ = "1.1.3"
diff --git a/plotsr/scripts/func.py b/plotsr/scripts/func.py
index 3801c14..97bfb7c 100755
--- a/plotsr/scripts/func.py
+++ b/plotsr/scripts/func.py
@@ -1714,7 +1714,10 @@ def drawmarkers(ax, b, v, chrlengths, indents, chrs, chrgrps, S, cfg, itx, minl=
                     ax.plot(m.start, indent-offset, marker=m.mt, color=m.mc, markersize=m.ms)
                     ax.text(m.start, indent-offset+m.tp, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='center', va='bottom')
                 else:
-                    ax.axhline(y=indent-offset, xmin=m.start/ax.get_xlim()[1], xmax=m.end/ax.get_xlim()[1], color=m.mc, linewidth=m.ms)
+                    # https://github.com/schneebergerlab/plotsr/issues/72
+                    # ax.axhline(y=indent-offset, xmin=m.start/ax.get_xlim()[1], xmax=m.end/ax.get_xlim()[1], color=m.mc, linewidth=m.ms)
+                    ax_xlim = ax.get_xlim()[1] - ax.get_xlim()[0]
+                    ax.axhline(y=indent-offset, xmin=(m.start-ax.get_xlim()[0])/ax_xlim, xmax=(m.end-ax.get_xlim()[0])/ax_xlim, color=m.mc, linewidth=m.ms, solid_capstyle='butt')
                     ax.text((m.start + m.end)/2, indent-offset+m.tp, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='center', va='bottom')
                 # if m.tt != '':
                 #     ax.text(m.start, indent-offset+m.tp, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='center', va='bottom')
@@ -1723,7 +1726,8 @@ def drawmarkers(ax, b, v, chrlengths, indents, chrs, chrgrps, S, cfg, itx, minl=
                     ax.plot(indent+offset, m.start, marker=m.mt, color=m.mc, markersize=m.ms)
                     ax.text(indent+offset-m.tp, m.start, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='left', va='center', rotation='vertical')
                 else:
-                    ax.axvline(x=indent+offset, ymin=m.start/ax.get_ylim()[1], ymax=m.end/ax.get_ylim()[1], color=m.mc, linewidth=m.ms)
+                    ax_ylim = ax.get_ylim()[1] - ax.get_ylim()[0]
+                    ax.axvline(x=indent+offset, ymin=(m.start - ax.get_ylim()[0])/ax_ylim, ymax=(m.end - ax.get_ylim()[0])/ax_ylim, color=m.mc, linewidth=m.ms, solid_capstyle='butt')
                     ax.text(indent+offset-m.tp, (m.start+m.end)/2, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='left', va='center', rotation='vertical')
                 # if m.tt != '':
                 #     ax.text(indent+offset-m.tp, m.start, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='left', va='center', rotation='vertical')
@@ -1736,6 +1740,7 @@ def drawmarkers(ax, b, v, chrlengths, indents, chrs, chrgrps, S, cfg, itx, minl=
                     ax.plot(m.start+buff[chrgrps[chrid][ind]], S - (step*ind), marker=m.mt, color=m.mc, markersize=m.ms)
                     ax.text(m.start+buff[chrgrps[chrid][ind]], S - (step*ind) + m.tp, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='center', va='bottom')
                 else:
+                    # TODO: Check and fix the issue reported in https://github.com/schneebergerlab/plotsr/issues/72
                     ax.axhline(y=S - (step*ind), xmin=(m.start+buff[chrgrps[chrid][ind]])/ax.get_xlim()[1], xmax=(m.end+buff[chrgrps[chrid][ind]])/ax.get_xlim()[1], color=m.mc, linewidth=m.ms)
                     ax.text(((m.start+m.end)/2)+buff[chrgrps[chrid][ind]], S - (step*ind) + m.tp, m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='center', va='bottom')
                 # if m.tt != '':
@@ -1745,6 +1750,7 @@ def drawmarkers(ax, b, v, chrlengths, indents, chrs, chrgrps, S, cfg, itx, minl=
                     ax.plot(1 - S + (step*ind), m.start+buff[chrgrps[chrid][ind]], marker=m.mt, color=m.mc, markersize=m.ms)
                     ax.text(1 - S + (step*ind)-m.tp, m.start+buff[chrgrps[chrid][ind]], m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='left', va='center', rotation='vertical')
                 else:
+                    # TODO: Check and fix the issue reported in https://github.com/schneebergerlab/plotsr/issues/72
                     ax.axvline(x=1 - S + (step*ind), ymin=(m.start+buff[chrgrps[chrid][ind]])/ax.get_ylim()[1], ymax=(m.end+buff[chrgrps[chrid][ind]])/ax.get_ylim()[1], color=m.mc, linewidth=m.ms)
                     ax.text(1 - S + (step*ind)-m.tp, ((m.start+m.end)/2)+buff[chrgrps[chrid][ind]], m.tt, color=m.tc, fontsize=m.ts, fontfamily=m.tf, ha='left', va='center', rotation='vertical')
                 # if m.tt != '':