From f779366d0dc8c584a719d36329a5fbc11717a7ca Mon Sep 17 00:00:00 2001
From: e-sollier <etienne.sollier@gmail.com>
Date: Wed, 21 Aug 2024 08:39:47 +0200
Subject: [PATCH] Add min height for sv track

---
 docs/content/describe_figure.rst   | 3 +++
 figeno/cli/cli.py                  | 2 +-
 figeno/gui/package.json            | 2 +-
 figeno/gui/src/Track.jsx           | 9 +++++++++
 figeno/gui/src/TracksContainer.jsx | 3 ++-
 figeno/track_sv.py                 | 8 +++++---
 pyproject.toml                     | 2 +-
 7 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/docs/content/describe_figure.rst b/docs/content/describe_figure.rst
index c188e14..3dace9b 100644
--- a/docs/content/describe_figure.rst
+++ b/docs/content/describe_figure.rst
@@ -373,6 +373,9 @@ Parameters:
 
 * ``color_del``, ``color_dup``, ``color_T2T``, ``color_H2H``, ``color_trans``: color of the arc representing the SV, depending on the SV type (respectively: deletion, duplication, tail-to-tail inversion, head-to-head inversion, translocation).
 
+* ``min_sv_height``: when a circular layout is used, minimum height of the SVs, between 0 and 1 (default: 0.1). Increasing this value will result in short SVs (where both breakends are close) to have a larger height.
+
+
 copynumber
 ^^^^^^^^^^
 
diff --git a/figeno/cli/cli.py b/figeno/cli/cli.py
index 8bfb8e0..20b558c 100644
--- a/figeno/cli/cli.py
+++ b/figeno/cli/cli.py
@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.4.5"
+__version__ = "1.4.6"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)
diff --git a/figeno/gui/package.json b/figeno/gui/package.json
index 6558fa0..c324e22 100644
--- a/figeno/gui/package.json
+++ b/figeno/gui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.4.5",
+  "version": "1.4.6",
   "private": true,
   "homepage": "./",
   "dependencies": {
diff --git a/figeno/gui/src/Track.jsx b/figeno/gui/src/Track.jsx
index f8c7c1c..688eee6 100644
--- a/figeno/gui/src/Track.jsx
+++ b/figeno/gui/src/Track.jsx
@@ -652,6 +652,15 @@ function SvTrack({track,set_value,openColorPanel, setFileDialogData,setFileDialo
             </div>
 
 
+        </div>
+        <div className="optionGroup">
+
+            <div className='formItem'>
+                <label htmlFor={"min_sv_height"+track.id}>Min SV height:</label>
+                <input id={"min_sv_height"+track.id} style={{width:"2em"}} value={track.min_sv_height}  onChange={(e) => set_value("min_sv_height",e.target.value)} ></input>
+            </div>
+
+
         </div>
             
         </>
diff --git a/figeno/gui/src/TracksContainer.jsx b/figeno/gui/src/TracksContainer.jsx
index c15778a..c4c6510 100644
--- a/figeno/gui/src/TracksContainer.jsx
+++ b/figeno/gui/src/TracksContainer.jsx
@@ -155,7 +155,8 @@ export const defaultTrackValues={
         color_dup:"#e55039",
         color_t2t:"#8e44ad",
         color_h2h:"#8e44ad",
-        color_trans:"#27ae60"
+        color_trans:"#27ae60",
+        min_sv_height:0.1
     },
     "copynumber":{
         height:"30",
diff --git a/figeno/track_sv.py b/figeno/track_sv.py
index 8df39e0..92e3a87 100644
--- a/figeno/track_sv.py
+++ b/figeno/track_sv.py
@@ -10,7 +10,7 @@
 
 class sv_track:
     def __init__(self,file=None,df_SVs=None,sv_across_regions=True,upside_down=False,label="BP",label_rotate=True,
-                 color_del="#4a69bd",color_dup="#e55039",color_h2h="#8e44ad",color_t2t="#8e44ad",color_trans="#27ae60",lw=0.6,
+                 color_del="#4a69bd",color_dup="#e55039",color_h2h="#8e44ad",color_t2t="#8e44ad",color_trans="#27ae60",lw=0.6,min_sv_height=0.1,
                  fontscale=1,bounding_box=True,height=10,margin_above=1.5,**kwargs):
         self.file=file
         self.df_SVs = df_SVs # Can directly provide a dataframe of SVs instead of providing a file (for use with python API).
@@ -24,7 +24,9 @@ def __init__(self,file=None,df_SVs=None,sv_across_regions=True,upside_down=False
         self.color_t2t=color_t2t
         self.color_trans=color_trans
         self.lw=float(lw)
-
+        self.min_sv_height=float(min_sv_height)
+        if self.min_sv_height>1: self.min_sv_height=1.0
+        if self.min_sv_height<0: self.min_sv_height=0.0
         self.fontscale=float(fontscale)
         self.bounding_box=bounding_box
         self.height = float(height)
@@ -131,7 +133,7 @@ def draw_circle(self, regions, box ,hmargin):
                     y = box["top"] if self.upside_down else box["bottom"] - 0.2
                     control_theta = (x1+x2)/2
                     control_r = 0
-                    if i==j: control_r = y * max(0,0.9-abs(df_SV_regions.loc[a,"pos1"]-df_SV_regions.loc[a,"pos2"]) / 400000000)
+                    if i==j: control_r = y * max(0,(1.0-self.min_sv_height)-abs(df_SV_regions.loc[a,"pos1"]-df_SV_regions.loc[a,"pos2"]) / 400000000)
 
                     pp1 = patches.PathPatch(mpath.Path([(x1, y), (control_theta, control_r), (x2, y)],[Path.MOVETO, Path.CURVE3, Path.CURVE3]),facecolor="none",edgecolor=df_SV_regions.loc[a,"color"])
                     boxes[0]["ax"].add_patch(pp1)
diff --git a/pyproject.toml b/pyproject.toml
index 7f57d4c..298f9c8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ packages = ["figeno", "figeno.data", "figeno.cli", "figeno.gui"]
 
 [project]
 name = 'figeno'
-version = "1.4.5"
+version = "1.4.6"
 description = 'Package for generating genomics figures.'
 readme = 'README.md'
 authors = [