--no_ntbiases option for Circos plots

Plots/nucleotide_biases.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 ## Pombert Lab, 2022
 my $name = 'nucleotide_biases.pl';
-my $version = '0.7a';
+my $version = '0.7b';
 my $updated = '2024-04-29';
 
 use strict;
@@ -57,6 +57,7 @@
 -max_points_per_track	Set max number of points per track [Default: 75000]
 -zdepth			Set links zdepth in ruleset [Default: 50]
 -clusters		Color by clusters [Default: off]
+-no_biases		Skip nucleotide bias subplots in Circos configuration files
 OPTIONS
 die "\n$usage\n" unless @ARGV;
 
@@ -83,6 +84,7 @@
 my $max_points_per_track = 75000;
 my $zdepth = 50;
 my $clusters;
+my $no_biases;
 GetOptions(
 	'f|fasta=s@{1,}' => \@fasta,
 	'o|outdir=s' => \$outdir,
@@ -106,7 +108,8 @@
 	'max_links=i' => \$max_links,
 	'max_points_per_track=i' => \$max_points_per_track,
 	'zdepth=i' => \$zdepth,
-	'clusters' => \$clusters
+	'clusters' => \$clusters,
+	'no_biases' => \$no_biases
 );
 
 ### List presets and stop
@@ -704,12 +707,19 @@ sub print_circos_conf {
 		}
 		print $cg 'chromosomes_units='.$unit_width."\n\n";
 
+
+
 		## Biases plots
+		my $r_start = 0.99;
+		my $r_end = 0.95;
+
+		if ($no_biases){
+			goto LINKS;
+		}
+
 		print $cg '<plots>'."\n";
 		print $cg '################# BIASES'."\n\n";
 
-		my $r_start = 0.99;
-		my $r_end = 0.95;
 		my $modulo_counter = 0;
 
 		for my $bias (@biases) {
@@ -739,6 +749,7 @@ sub print_circos_conf {
 
 		print $cg '</plots>'."\n\n";
 
+		LINKS:
 		unless ($link_status eq 'nolink'){
 
 			my $link_start = $r_end + 0.04;

README.md

@@ -258,6 +258,7 @@ Options for run_SYNY.pl are:
 --max_links             Set max number of links [Default: 25000]
 --max_points_per_track  Set max number of points per track [Default: 75000]
 --clusters              Color by cluster instead of contig/chromosome [Default: off]
+--no_ntbiases           Turn off nucleotide biases subplots
 --no_cticks             Turn off ticks in Circos plots
 --no_circos             Turn off Circos plots
 
@@ -547,11 +548,15 @@ Karyotypes can be plotted with Circos in normal and/or inverted orientation(s).
   <img src="https://github.com/PombertLab/SYNY/blob/main/Images/WM276_vs_JEC21.gap_0.normal.png">
 </p>
 
-In this figure, nucleotides biases are plotted in the concentric rings (from outer to inner rings):
+In this figure, nucleotides biases are plotted in the concentric rings. These subplots can be skipped with the `--no_ntbiases` command line switch. From from outer to inner, the concentric rings are:
+
 - AT and GC nucleotide biases (grey and red lines)
 - GT and AC nucleotide biases (blue and green lines)
 - GA and CT nucleotide biases (purple and yellow lines)
 
+
+
+
 Syntenic blocks identified by SYNY are indicated by ribbons. These ribbons are color-coded based on the chromosomes/contigs present in the reference genome used. If desired, color coding can be set by cluster instead with `--clusters`. This option is useful when working with prokaryotes featuring a single chromosome, so that the ribbons are not all of the same color.
 
 By default, contigs will be labelled by arabic and roman numerals in the Circos plots. Contigs from the reference (query) are labelled by roman numerals; others are labelled by arabic numerals. If desired, contigs can instead be labelled by their names with the `--labels names` command line option. Label sizes (default: 36) and fonts can be further adjusted with the `--label_size` and `--label_font` command line options. Possible fonts are: `light`, 

run_syny.pl

@@ -2,7 +2,7 @@
 # Pombert lab, 2022
 
 my $name = 'run_syny.pl';
-my $version = '0.6.4f';
+my $version = '0.6.5';
 my $updated = '2024-04-29';
 
 use strict;
@@ -71,6 +71,7 @@
 --max_links		Set max number of links [Default: 25000]
 --max_points_per_track	Set max number of points per track [Default: 75000]
 --clusters		Color by cluster instead of contig/chromosome [Default: off]
+--no_ntbiases		Turn off nucleotide biases subplots
 --no_cticks		Turn off ticks in Circos plots
 --no_circos		Turn off Circos plots
 
@@ -137,6 +138,7 @@
 my $max_points_per_track = 75000;
 my $clusters;
 my $circos_orientation = 'normal';
+my $no_ntbiases;
 my $no_circos;
 my $no_cticks;
 
@@ -198,6 +200,7 @@
 	'max_points_per_track=i' => \$max_points_per_track,
 	'clusters' => \$clusters,
 	'orientation=s' => \$circos_orientation,
+	'no_ntbiases' => \$no_ntbiases,
 	'no_circos' => \$no_circos,
 	'no_cticks' => \$no_cticks,
 	# Barplots
@@ -1079,6 +1082,11 @@
 	$circos_ticks_flag = '--noticks';
 }
 
+my $circos_ntbiases_flag = '';
+if ($no_ntbiases){
+	$circos_ntbiases_flag = '--no_biases';
+}
+
 my $gap = $gaps[0];
 
 ## Running nucleotide_biases.pl
@@ -1101,6 +1109,7 @@
 	--max_points_per_track $max_points_per_track \\
 	$cluster_flag \\
 	$circos_ticks_flag \\
+	$circos_ntbiases_flag \\
 	2>> $log_err
 ") == 0 or checksig();