Improve chr label positition for circos plots

Author: e-sollier

figeno/figeno.py

@@ -138,7 +138,7 @@ def __init__(self,config=None,config_file=None,reference=None,genes_file=None,ch
                         t["genes_file"] = self.genes_file
                         self.tracks_list.append(ase_track(**t))
                     else:
-                        pass
+                        print("WARNING: unrecognized track type: "+str(t))
 
             self.figure_layout = config["general"]["layout"]
             self.output = None
@@ -256,7 +256,7 @@ def draw_horizontal(self,file,width=183,dpi=150,transparent=False):
             current_height+=t.height+t.margin_above
         plt.axis('off')
         #fig.savefig(outfile,bbox_inches="tight",pad_inches=0.0,dpi=dpi)
-        plt.tight_layout(pad=0)
+        plt.tight_layout(pad=0.1)
         fig.savefig(file,dpi=dpi,transparent=transparent)
         plt.cla() 
         plt.clf() 
@@ -292,7 +292,7 @@ def draw_stacked(self,file,width=183,dpi=150,transparent=False):
             current_height+=t.height+t.margin_above
         plt.axis('off')
         #fig.savefig(outfile,bbox_inches="tight",pad_inches=0.0,dpi=dpi)
-        plt.tight_layout(pad=0)
+        plt.tight_layout(pad=0.1)
         fig.savefig(file,dpi=dpi,transparent=transparent)
         plt.cla() 
         plt.clf() 
@@ -337,7 +337,7 @@ def draw_symmetrical(self,file,width=183,dpi=150,transparent=False):
 
             current_height+=t.height
         plt.axis('off')
-        plt.tight_layout(pad=0)
+        plt.tight_layout(pad=0.1)
         fig.savefig(file,dpi=dpi,transparent=transparent)
         plt.cla() 
         plt.clf() 
@@ -383,7 +383,7 @@ def draw_circular(self,file,width=183,dpi=150,transparent=False):
         plt.axis('off')
         ax.set_rmin(0)
         ax.set_rmax(current_r)
-        plt.tight_layout(pad=0)
+        plt.tight_layout(pad=0.1)
         fig.savefig(file,dpi=dpi,transparent=transparent)
         plt.cla() 
         plt.clf() 

figeno/track_chr.py

@@ -289,10 +289,10 @@ def draw_region_circos(self,region,box):
         # label the region (need to rotate the text)
         rotation_text,halign,valign = compute_rotation_text((box["left"]+box["right"])/2)
 
-        r_text = r_rec+(box["top"]-box["bottom"])*0.1
-
-        box["ax"].text((box["left"]+box["right"])/2,r_text,region.chr,rotation=rotation_text,verticalalignment=valign,horizontalalignment=halign,fontsize=22*self.fontscale)
+        r_text = r_rec+(box["top"]-box["bottom"])*0.4
 
+        #box["ax"].text((box["left"]+box["right"])/2,r_text,region.chr,rotation=rotation_text,verticalalignment=valign,horizontalalignment=halign,fontsize=22*self.fontscale)
+        box["ax"].text((box["left"]+box["right"])/2,r_text,region.chr,rotation=rotation_text,verticalalignment="center",horizontalalignment="center",fontsize=22*self.fontscale)
         #,bbox=dict(facecolor='red', alpha=0.4, edgecolor='black')
 
     def get_highlights_offsets(self):