removing text from columns optionally with --remove-site-text

snipit/command.py

@@ -62,6 +62,7 @@ def main(sysargs = sys.argv[1:]):
     f_group.add_argument("--high-to-low", action='store_false',
                         help="If sorted by mutation number is selected, show the sequences with the fewest SNPs closest to the reference. Default: False",
                         dest="high_to_low")
+    f_group.add_argument("--remove-site-text",action='store_true',help="Do not annotate text on the individual columns in the figure.",dest="remove_site_text")
 
     s_group = parser.add_argument_group('SNP options')
     s_group.add_argument("--show-indels",action='store_true',help="Include insertion and deletion mutations in snipit plot.",dest="show_indels")
@@ -128,10 +129,11 @@ def main(sysargs = sys.argv[1:]):
                         args.height,
                         args.size_option,
                         args.solid_background,
+                        args.remove_site_text,
+                        args.ambig_mode,
                         args.flip_vertical,
                         args.included_positions,
                         args.excluded_positions,
-                        args.ambig_mode,
                       args.sort_by_mutation_number,
                       args.high_to_low,
                       args.sort_by_id,

snipit/scripts/snp_functions.py

@@ -376,6 +376,7 @@ def make_graph(num_seqs,
                 height,
                 size_option,
                 solid_background,
+                remove_site_text,
                 ambig_mode,
                flip_vertical=False,
                included_positions=None,
@@ -543,7 +544,7 @@ def make_graph(num_seqs,
     fig, ax = plt.subplots(1,1, figsize=(width,height), dpi=250)
 
     y_level = 0
-
+    print(remove_site_text)
     for record in record_order:
 
         # y position increments, with a gap after the two recombi_refs
@@ -570,7 +571,8 @@ def make_graph(num_seqs,
 
         # write text adjacent to the SNPs shown with the numeric position
         # the text alignment is toggled right/left (top/bottom considering 90-deg rotation) if the plot is flipped
-        ax.text(position, y_level+(0.55*y_inc), snp, size=9, ha="center", va="bottom" if not flip_vertical else "top", rotation=90)
+        if not remove_site_text:
+            ax.text(position, y_level+(0.55*y_inc), snp, size=9, ha="center", va="bottom" if not flip_vertical else "top", rotation=90)
 
         # snp position labels
         left_of_box = position-(0.4*spacing)
@@ -594,11 +596,12 @@ def make_graph(num_seqs,
             ax.add_patch(rect)
 
             # sequence variant text
-            ax.text(position, y_pos*y_inc, var, size=9, ha="center", va="center")
+            if not remove_site_text:
+                ax.text(position, y_pos*y_inc, var, size=9, ha="center", va="center")
 
         # reference variant text
-
-        ax.text(position, y_inc * -0.2, ref, size=9, ha="center", va="center")
+        if not remove_site_text:
+            ax.text(position, y_inc * -0.2, ref, size=9, ha="center", va="center")
 
         #polygon showing mapping from genome to spaced out snps
         x = [snp-0.5,snp+0.5,right_of_box,left_of_box,snp-0.5]