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Plot the clock using Lastz -gerenal outfile

  • Public
By Jit 32 days ago
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() ;