Add support for strand information in bed tracks

docs/content/describe_figure.rst

@@ -135,6 +135,8 @@ Parameters:
 
 * ``show_names``: if True, will display the name of each region above the corresponding rectangle. This requires that the bed file contains a fourth column indicating the name of each region.
 
+* ``show_strand``: if True, will display arrows indicating the strand of each region. This requires that the bed file contains a sixth column indicating the strand of each region ("+", "-", or ".").
+
 bigwig
 ^^^^^^^^
 

figeno/gui/src/Track.jsx

@@ -216,6 +216,10 @@ function BedTrack({track,set_value,openColorPanel, setFileDialogData,setFileDial
                 <label htmlFor={"show_names"+track.id}>Show names:</label>
                 <input type="checkbox" id={"show_names"+track.id} checked={track.show_names} onChange={() => set_value("show_names",!track.show_names)} ></input>
             </div>
+            <div className='formItem'>
+                <label htmlFor={"show_strand"+track.id}>Show strand:</label>
+                <input type="checkbox" id={"show_strand"+track.id} checked={track.show_strand} onChange={() => set_value("show_strand",!track.show_strand)} ></input>
+            </div>
 
         </div>
         </>

figeno/gui/src/TracksContainer.jsx

@@ -35,13 +35,14 @@ export const defaultTrackValues={
         show_gene_names:true
     },
     "bed":{
-        height:"10",
+        height:"3",
         margin_above:"1.5",
         bounding_box:false,
         fontscale:1.0,
         file:"",
         color:"#444444",
         show_names:false,
+        show_strand:false,
         label:"",
         label_rotate:false
     },

figeno/track_bed.py

@@ -7,12 +7,13 @@
 
 
 class bed_track:
-    def __init__(self,file,color="#051650",label="",label_rotate=False,show_names=False,fontscale=1,bounding_box=False,height=6,margin_above=1.5,**kwargs):
+    def __init__(self,file,color="#051650",label="",label_rotate=False,show_names=False,show_strand=False,fontscale=1,bounding_box=False,height=3,margin_above=1.5,**kwargs):
         self.file = file
         self.color=color
         self.label=label
         self.label_rotate=label_rotate
         self.show_names = show_names
+        self.show_strand=show_strand
         self.fontscale=float(fontscale)
         self.bounding_box=bounding_box
         self.height = float(height)
@@ -27,6 +28,13 @@ def draw(self, regions, box ,hmargin,warnings):
         if not os.path.isfile(self.file):
             raise KnownException("The following bed file could not be found: "+self.file)
 
+        # Make sure that the file can be read
+        try:
+            with open(self.file,"r") as infile:
+                line=infile.readline()
+        except:
+            raise KnownException("The following bed file could not be read: "+self.file)
+
         boxes = split_box(box,regions,hmargin)
         for i in range(len(regions)):
             self.draw_region(regions[i][0],boxes[i],warnings)
@@ -37,7 +45,6 @@ def draw(self, regions, box ,hmargin,warnings):
 
     def draw_region(self,region,box,warnings):
         if self.bounding_box: draw_bounding_box(box)
-
 
         if self.show_names: 
             rect_height = (box["top"]-box["bottom"]) * 0.4
@@ -46,8 +53,15 @@ def draw_region(self,region,box,warnings):
             rect_height = (box["top"]-box["bottom"]) * 0.7
             rect_bottom = box["bottom"] +  (box["top"]-box["bottom"]) * 0.15
 
+        # Params for strand
+        self.arrow_gapwidth=3 # gap between arrows
+        self.arrow_height=min(0.8*rect_height,1.4)
+        self.arrow_width=min(0.5,1.5*self.arrow_height)
+
+
         with open(self.file,"r") as infile:
             for line in infile:
+                if line.startswith("#"): continue
                 linesplit = line.rstrip("\n").split("\t")
                 if len(linesplit)<3: raise KnownException("The following bed file has the wrong format: "+self.file+".\nThe file should be tab-separated, without header, with at least 3 columns: chr, start, end.\nProblematic line:\n"+line[:70])
                 if linesplit[0].lstrip("chr")==region.chr.lstrip("chr"):
@@ -64,16 +78,46 @@ def draw_region(self,region,box,warnings):
                             converted_end = box["right"] - (start-region.start) / (region.end-region.start) * (box["right"] - box["left"])
                         converted_start = min(box["right"],max(box["left"],converted_start))
                         converted_end = min(box["right"],max(box["left"],converted_end))
+                        rect_width=converted_end-converted_start
 
-                        rect = patches.Rectangle((converted_start,rect_bottom),converted_end-converted_start,rect_height,color=self.color)
+                        rect = patches.Rectangle((converted_start,rect_bottom),rect_width,rect_height,color=self.color)
                         box["ax"].add_patch(rect)
 
+
                         if self.show_names:
                             if len(linesplit)>3:
                                 box["ax"].text((converted_start+converted_end)/2,(rect_bottom+rect_height+1),linesplit[3],
                                            horizontalalignment="center",verticalalignment="bottom",fontsize=8*self.fontscale)
                             else: 
                                 warnings.append("For the bed file "+self.file+", you ticked the show_names option, but no names were found for line "+line +" (should be the 4th column).")
+
+
+                        if self.show_strand:
+                            arrow_center=rect_bottom+rect_height/2
+                            arrow_bottom=arrow_center-self.arrow_height/2
+                            arrow_top=arrow_center+self.arrow_height/2
+                            if len(linesplit)>5:
+                                strand=linesplit[5]
+                                if not strand in ["+","-"]: continue
+                                if rect_width<1.2*self.arrow_width: continue
+                                # Number of arrows that can fit in the rectangle
+                                n_arrows= 1+ int((rect_width-3*self.arrow_width)/(self.arrow_gapwidth+self.arrow_width))
+
+                                if rect_width<3*self.arrow_width:
+                                    current_left_pos=(converted_start+converted_end)/2 - self.arrow_width/2
+                                else:
+                                    arrows_width= 3*self.arrow_width + (n_arrows-1)*(self.arrow_gapwidth+self.arrow_width)
+                                    current_left_pos=(converted_start+converted_end)/2 -arrows_width/2 + self.arrow_width
+                                for i in range(n_arrows):
+                                    if strand=="+":
+                                        box["ax"].plot([current_left_pos,current_left_pos+self.arrow_width,current_left_pos],[arrow_top,arrow_center,arrow_bottom],color="white",lw=0.4,zorder=3)
+                                    else:
+                                        box["ax"].plot([current_left_pos+self.arrow_width,current_left_pos,current_left_pos+self.arrow_width],[arrow_top,arrow_center,arrow_bottom],color="white",lw=0.4,zorder=3)
+                                    current_left_pos+=self.arrow_gapwidth+self.arrow_width
+                            else:
+                                warnings.append("For the bed file "+self.file+", you ticked the show_strand option, but no strand information was found for line "+line +" (should be the 6th column).")
+
+
     def draw_title(self,box):
         if len(self.label)>0:
             self.label = self.label.replace("\\n","\n")