Plot the clock using Lastz -gerenal outfile

Jit — Thu, 18 Jan 2018 11:05:25 -0600

use strict;
use warnings;
use Statistics::R ;
use List::Util qw(sum);

#Usage  perl clockPlot.pl Palindrome.palfc 1500
my $R = Statistics::R->new() ;
$R->startR ;

my $fileN=$ARGV[0];
my $mSize=$ARGV[1];
open (my $fh2, $fileN) or die "Could not open file $fileN $!";
my (@allKeys, @allFreq); my %pHash;
while(<$fh2>) {
	chomp;
	next if /^$/; #next if empty
	my @arr = split("\t", $_);
	if ($arr[7] eq "-") {
		my $len=$arr[5]-$arr[4];
		#next if $len < $mSize;
		my @chr = split '\_', $arr[1];
		$chr[0] =~ s/[a-z]//g;
		my $newChr="$chr[0]"."_"."$arr[3]";
		$pHash{$newChr}++;
	}
}

foreach my $val (keys %pHash) {
	#next if $pHash{$val} > 10;
	my @sChr = split '\_', $val;
	my $score=$pHash{$val}/$sChr[1];
	push @allKeys, $sChr[0];
	push @allFreq, $score;
}

my $allKeys=join ',', @allKeys;
my $allFreq=join ',', @allFreq;
my $hLen=scalar (@allKeys);
my $ll="$hLen".'L';

$R->run(qq`
d <- structure(list(Chromosome = c($allKeys), Frequency = c($allFreq)), .Names = c("Chromosome", "Frequency"
), row.names = c(NA, $ll), class = "data.frame")
str(d)

library(ggplot2)
ggplot(d , aes(x =  Chromosome, y =  Frequency, fill=Frequency)) +
  coord_polar(theta = "x", start = -pi/5) +
  geom_bar(stat = "identity") + 
  scale_x_continuous(breaks = seq(0, $hLen, 50))`);

$R->stopR() ;

BOL: Plot the clock using Lastz -gerenal outfile

Plot the clock using Lastz -gerenal outfile