Add option for custom chr_prefix

Author: e-sollier

docs/content/describe_figure.rst

@@ -93,6 +93,7 @@ Parameters:
 
 * ``ticks_angle``: Angle in degrees at which the ticks are written. The default (0) results in horizontal ticks, but you can also tilt them by increasing this value to e.g. 30. Rotating the ticks might result in them overlapping with the chromosome name, so you might want to post-process the figure in a vector graphics editor by manualling moving the chromosome name in case of overlap.
 
+* ``chr_prefix``: Prefix to add before the chromosome names (default: "chr").
 
 genes
 ^^^^^  

figeno/cli/cli.py

@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.4.7"
+__version__ = "1.5.0"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

figeno/gui/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.4.7",
+  "version": "1.5.0",
   "private": true,
   "homepage": "./",
   "dependencies": {

figeno/gui/package.json

@@ -148,6 +148,10 @@ function ChrTrack({track,set_value}){
             <div className='formItem'>
                 <label htmlFor={"ticks_angle"+track.id}>Ticks angle (°):</label>
                 <input id={"ticks_angle"+track.id} style={{width:"3em"}} value={track.ticks_angle}  onChange={(e)=>set_value("ticks_angle",e.target.value)} ></input>
+            </div>
+            <div className='formItem'>
+                <label htmlFor={"chr_prefix"+track.id}>Chr prefix:</label>
+                <input id={"chr_prefix"+track.id} style={{width:"3em"}} value={track.chr_prefix}  onChange={(e)=>set_value("chr_prefix",e.target.value)} ></input>
             </div> 
             </>):""}
         </div>

figeno/gui/src/Track.jsx

@@ -18,7 +18,8 @@ export const defaultTrackValues={
         ticklabels_pos:"below",
         unit:"kb",
         ticks_interval:"auto",
-        ticks_angle:0
+        ticks_angle:0,
+        chr_prefix: "chr"
     },
     "genes":{
         height:"10",

figeno/gui/src/TracksContainer.jsx

@@ -9,7 +9,7 @@
 from figeno.utils import KnownException, split_box, draw_bounding_box , interpolate_polar_vertices, compute_rotation_text, polar2cartesian, cartesian2polar
 
 class chr_track:
-    def __init__(self,style="default",unit="kb",ticklabels_pos="below",ticks_interval="auto",ticks_angle=0,lw_scale=1.0,no_margin=False,reference="custom",cytobands_file="",
+    def __init__(self,style="default",unit="kb",ticklabels_pos="below",ticks_interval="auto",ticks_angle=0,lw_scale=1.0,chr_prefix="chr",no_margin=False,reference="custom",cytobands_file="",
                  fontscale=1,bounding_box=False,height=12,margin_above=1.5,label="",label_rotate=False,**kwargs):
         self.style=style
         self.unit=unit
@@ -19,6 +19,7 @@ def __init__(self,style="default",unit="kb",ticklabels_pos="below",ticks_interva
         self.lw_scale= float(lw_scale)
         while self.ticks_angle<-180: self.ticks_angle+=360
         while self.ticks_angle>180: self.ticks_angle-=360
+        self.chr_prefix=chr_prefix
         self.no_margin=no_margin
         self.reference=reference
         self.fontscale=float(fontscale)
@@ -149,9 +150,9 @@ def draw_region(self,region,box,single_region=False):
         # Chr label
         if self.ticklabels_pos!="none":
             if self.ticklabels_pos=="below" and (not "upside_down" in box):
-                box["ax"].text((box["left"]+box["right"])/2,box["bottom"],"chr"+region.chr,horizontalalignment="center",verticalalignment="bottom",fontsize=9*self.fontscale)
+                box["ax"].text((box["left"]+box["right"])/2,box["bottom"],self.chr_prefix+region.chr,horizontalalignment="center",verticalalignment="bottom",fontsize=9*self.fontscale)
             else:
-                box["ax"].text((box["left"]+box["right"])/2,box["top"],"chr"+region.chr,horizontalalignment="center",verticalalignment="top",fontsize=9*self.fontscale)
+                box["ax"].text((box["left"]+box["right"])/2,box["top"],self.chr_prefix+region.chr,horizontalalignment="center",verticalalignment="top",fontsize=9*self.fontscale)
 
     def draw_region_arrow(self,region,box):
         arrow_height = (box["top"]-box['bottom']) * 0.5 *self.lw_scale
@@ -193,23 +194,23 @@ def draw_region_arrow(self,region,box):
                            fontsize=8*self.fontscale)
 
         if self.ticklabels_pos=="below" and (not "upside_down" in box):
-            box["ax"].text((box["right"]+box["left"])/2,box["top"]-arrow_height*1.55,"chr"+region.chr.lstrip("chr"),horizontalalignment="center",verticalalignment="top",
+            box["ax"].text((box["right"]+box["left"])/2,box["top"]-arrow_height*1.55,self.chr_prefix+region.chr.lstrip("chr"),horizontalalignment="center",verticalalignment="top",
                            fontsize=10*self.fontscale)
         else:
-            box["ax"].text((box["right"]+box["left"])/2,box["bottom"]+arrow_height*1.55,"chr"+region.chr.lstrip("chr"),horizontalalignment="center",verticalalignment="bottom",
+            box["ax"].text((box["right"]+box["left"])/2,box["bottom"]+arrow_height*1.55,self.chr_prefix+region.chr.lstrip("chr"),horizontalalignment="center",verticalalignment="bottom",
                            fontsize=10*self.fontscale)
 
     def draw_region_ideogram(self,region,box):
         height = (box["top"]-box["bottom"]) * 0.5 *self.lw_scale
         if self.ticklabels_pos=="below" and (not "upside_down" in box):
             y = box["bottom"] + (box["top"]-box["bottom"]) * 0.75
             if self.fontscale>0:
-                box["ax"].text((box["left"]+box["right"])/2, box["top"]-height-1, "chr"+region.chr,
+                box["ax"].text((box["left"]+box["right"])/2, box["top"]-height-1, self.chr_prefix+region.chr,
                            horizontalalignment="center", verticalalignment="top",fontsize=10*self.fontscale)
         elif self.ticklabels_pos=="above":
             y = box["bottom"] + (box["top"]-box["bottom"]) * 0.25
             if self.fontscale>0:
-                box["ax"].text((box["left"]+box["right"])/2, box["bottom"] + height+1, "chr"+region.chr,
+                box["ax"].text((box["left"]+box["right"])/2, box["bottom"] + height+1, self.chr_prefix+region.chr,
                            horizontalalignment="center", verticalalignment="bottom",fontsize=10*self.fontscale)
         else:
             y= (box["bottom"]+box["top"]) / 2

figeno/track_chr.py

@@ -9,7 +9,7 @@ packages = ["figeno", "figeno.data", "figeno.cli", "figeno.gui"]
 
 [project]
 name = 'figeno'
-version = "1.4.7"
+version = "1.5.0"
 description = 'Package for generating genomics figures.'
 readme = 'README.md'
 authors = [