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RNAseq_graph.pl
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#!/usr/bin/perl -w
use strict;
## genes.fpkm_tracking
## tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status q3_FPKM q3_conf_lo q3_conf_hi q3_status
## ChrSy.fgenesh.gene.1 - - ChrSy.fgenesh.gene.1 ChrSy.fgenesh.gene.1 - chrSy:784-1168 - - 0 0 0 OK 0 0 0 OK 0 0 0 OK
my $top_dir = shift;
opendir my ($dh), $top_dir or die "Couldn't open dir '$top_dir': $!";
my @files = readdir $dh;
closedir $dh;
my %order;
my %fpkm;
foreach my $dir (@files) {
next unless -d "$top_dir/$dir";
my ( $run_info, $fpkm_file );
if ( -e "$top_dir/$dir/run.info" and -e "$top_dir/$dir/genes.fpkm_tracking" )
{
$run_info = "$top_dir/$dir/run.info";
$fpkm_file = "$top_dir/$dir/genes.fpkm_tracking";
} else {
next;
}
my @order;
my $group;
open INFO, $run_info or die "Can't open $run_info\n";
while ( my $line = <INFO> ) {
chomp $line;
next unless $line =~ /cmd_line/;
($group) = $line =~ /\-o\s+(\S+)/;
my @bams = $line =~ /(\S+\.bam)/g;
foreach my $bam (@bams) {
if ( $bam =~ /NB/ ) {
push @order, 'NB';
} elsif ( $bam =~ /HEG/ ) {
push @order, 'HEG4';
} else {
push @order, 'EG4';
}
}
}
$order{$group}{ $order[0] } = 'q1';
$order{$group}{ $order[1] } = 'q2';
$order{$group}{ $order[2] } = 'q3';
open IN, $fpkm_file or die "Can't open $fpkm_file\n";
while ( my $line = <IN> ) {
chomp $line;
next if $line =~ /^tracking_id/;
my @line = split "\t", $line;
my $gene = $line[0];
my $q1_FPKM = $line[9];
my $q2_FPKM = $line[13];
my $q3_FPKM = $line[17];
foreach my $strain ( keys %{ $order{$group} } ) {
if ( $order{$group}{$strain} eq 'q1' ) {
$fpkm{$gene}{$group}{$strain} = $q1_FPKM;
} elsif ( $order{$group}{$strain} eq 'q2' ) {
$fpkm{$gene}{$group}{$strain} = $q2_FPKM;
} elsif ( $order{$group}{$strain} eq 'q3' ) {
$fpkm{$gene}{$group}{$strain} = $q3_FPKM;
}
}
}
}
my $count = 0;
#my $dir_count = 0;
my $new_dir = "RNASeq_images";
if ( !-d $new_dir ) {
`mkdir -p $new_dir`;
}
foreach my $gene ( sort keys %fpkm ) {
my @dataframe;
my ($subdir) = $gene =~ /^(.{8})/; #LOC_Os1
my $new_dir = "RNASeq_images/$subdir";
my @values;
`mkdir -p $new_dir` if !-e $new_dir;
next if -e "$new_dir/$gene.RNASeq.png";
open OUTR, ">$new_dir/$gene.RNASeq.R"
or die "Cant open $new_dir/$gene.RNASeq.R";
print OUTR
qq(png(file = "$new_dir/$gene.RNASeq.png", bg = "transparent")\n
par(mar=c(5.1, 4.1, 4.1, 8.1), xpd=TRUE)\n);
#my %dataframe;
foreach my $group ( sort keys %{ $fpkm{$gene} } ) {
my $NB_FPKM = $fpkm{$gene}{$group}{NB};
my $HEG4_FPKM = $fpkm{$gene}{$group}{HEG4};
my $EG4_FPKM = $fpkm{$gene}{$group}{EG4};
print OUTR "$group <- c(", join( ',', $NB_FPKM, $EG4_FPKM, $HEG4_FPKM ),")\n";
push @dataframe, $group;
}
my $colors = scalar @dataframe;
my $dataframe = join ",", @dataframe;
print OUTR
qq(colorlist <- append ( colors()[grep("medium",colors())] , colors()[grep("dark",colors())] )\n
plot_colors <- c(colorlist[1:$colors])\n
data <- data.frame($dataframe)\n
max_y <- max(data)\n);
my $first_dataframe = shift @dataframe;
my $pch = 0;
print OUTR
qq(plot(data\$$first_dataframe,type = "b",pch=$pch,col=plot_colors[1],ylim=c(0,max_y),axes=FALSE,ann=FALSE)\n
axis(1,at=1:3,lab=c(\"NB\",\"EG4\",\"HEG4\"))\n
axis(2,las=1, at=1*0:max_y)\n
box()\n);
my $i = 2;
foreach my $df (@dataframe) {
if ( $pch == 25 ) {
$pch = 0;
} else {
$pch++;
}
print OUTR qq(points(data\$$df, type="b",pch=$pch,col=plot_colors[$i])\n);
$i++;
}
print OUTR qq (
title(main= paste(strwrap("Gene expression in different Conditions and Strains for $gene",width=50),collapse="\\n"),col.main="black", font.main=2)\n
title(xlab= "Strains", col.lab=rgb(0,0,0))\n
title(ylab= "FPKM", col.lab=rgb(0,0,0))\n
legend(3.1, max_y, names(data), cex=0.8, col=plot_colors, pch=0:$colors)\n
dev.off()\n);
close OUTR;
`Rscript "$new_dir/$gene.RNASeq.R"`;
}
__END__
#my %conditions =
#(cold_day1_1hr_control => "aliceblue", "cold_day1_3hr_control" => "azure","cold_day2_1hr_control"=>"blue","cold_day2_3hr_control"=>"blueviolet","cold_day3_1hr_control"=>"cadetblue","cold_day3_3hr_control"=>"cornflowerblue","cold_day1_1hr_exp"=>"cyan","cold_day1_3hr_exp"=>"darkblue","cold_day2_1hr_exp"=>"darkcyan","cold_day2_3hr_exp"=>"darkslate","cold_day3_1hr_exp"=>"darkturquois","cold_day3_3hr_exp"=>"deepskyblue","salt_0.5hr_control"=>"antiquewhite","salt_2hr_control"=>"beige","salt_10hr_control"=>"bisque","salt_24hr_control"=>"blanchedalmond","salt_48hr_control"=>"burlywood","salt_30min_control"=>"burlywood1","salt_30min_150mM"=>"burlywood4","salt_2hr_150mM"=>"wheat","salt_10hr_150mM"=>"floralwhite","salt_24hr_150mM"=>"lemonchiffon","salt_48hr_150mM"=>"lightgoldenrod","drought_0hr_control"=>"violetred1","drought_1hr_control"=>"tomato","drought_5hr_exp"=>"pink","drought_10hr_exp"=>"paleviletred","drought_24hr_exp"=>"salmon","drought_48hr_exp"=>"rosybrown1","drought_a"=>"orangered","drought_b"=>"red","drought_c"=>"lightsalmon","drought_d"=>"lightpink","drought_e"=>"lightcoral","drought_f"=>"indianred","drought_g"=>"hotpink");