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MNSMAR / CLIPSeqTools-1.0.0 / lib / CLIPSeqTools / PlotApp / libraries_relative_read_density.pm 

            

              
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=head1 NAME
CLIPSeqTools::PlotApp::libraries_relative_read_density - Create plots for
script libraries_relative_read_density.
=head1 SYNOPSIS
clipseqtools-plot libraries_relative_read_density [options/parameters]
=head1 DESCRIPTION
Create plots for script libraries_relative_read_density.
=head1 OPTIONS
  Input.
    --file <Str>           input file.
  Output
    --o_prefix <Str>       output path prefix. Script will create and add
                           extension to path. [Default: ./]
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message
=cut
package CLIPSeqTools::PlotApp::libraries_relative_read_density;
$CLIPSeqTools::PlotApp::libraries_relative_read_density::VERSION = '1.0.0';
# Make it an app command
use MooseX::App::Command;
extends 'CLIPSeqTools::PlotApp';
#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;
use autodie;
use namespace::autoclean;
use Statistics::R;
#######################################################################
#######################   Command line options   ######################
#######################################################################
option 'file' => (
        is            => 'rw',
        isa           => 'Str',
        required      => 1,
        documentation => 'input file.',
);
#######################################################################
##########################   Consume Roles   ##########################
#######################################################################
with
        "CLIPSeqTools::Role::Option::OutputPrefix" => {
                -alias    => { validate_args => '_validate_args_for_output_prefix' },
                -excludes => 'validate_args',
        };
#######################################################################
########################   Interface Methods   ########################
#######################################################################
sub validate_args {
        my ($self) = @_;
        $self->_validate_args_for_output_prefix;
}
sub run {
        my ($self) = @_;
        warn "Validating arguments\n" if $self->verbose;
        $self->validate_args();
        warn "Creating output path\n" if $self->verbose;
        $self->make_path_for_output_prefix();
        warn "Creating plots with R\n" if $self->verbose;
        $self->run_R;
}
sub run_R {
        my ($self) = @_;
        my $figfile = $self->o_prefix . 'libraries_relative_read_density.pdf';
        # Start R
        my $R = Statistics::R->new();
        # Pass arguments to R
        $R->set('ifile', $self->file);
        $R->set('figfile', $figfile);
        # Read table with data
        $R->run(q{idata = read.delim(ifile)});
        # Convert counts to density
        $R->run(q{idata$norm_counts_with_copy_number_sense =
                idata$counts_with_copy_number_sense /
                (sum(as.numeric(idata$counts_with_copy_number_sense)) + 1)});
        $R->run(q{idata$norm_counts_no_copy_number_sense =
                idata$counts_no_copy_number_sense /
                (sum(as.numeric(idata$counts_no_copy_number_sense)) + 1)});
        $R->run(q{idata$norm_counts_with_copy_number_antisense =
                idata$counts_with_copy_number_antisense /
                (sum(as.numeric(idata$counts_with_copy_number_antisense)) + 1)});
        $R->run(q{idata$norm_counts_no_copy_number_antisense =
                idata$counts_no_copy_number_antisense /
                (sum(as.numeric(idata$counts_no_copy_number_antisense)) + 1)});
        # Find plot y_lim
        $R->run(q{ylimit = max(idata$norm_counts_with_copy_number_sense,
                idata$norm_counts_no_copy_number_sense,
                idata$norm_counts_with_copy_number_antisense,
                idata$norm_counts_no_copy_number_antisense)});
        # Do plots
        $R->run(q{pdf(figfile, width=28)});
        $R->run(q{par(mfrow = c(1, 4), cex.lab=1.8, cex.axis=1.7, cex.main=2,
                lwd=1.5, oma=c(0, 0, 2, 0))});
        $R->run(q{plot(idata$relative_position,
                idata$norm_counts_with_copy_number_sense, type="o", main="Sense
                records (with copy number)", xlab="Relative position", ylab="Density",
                col="darkred", ylim=c(0,ylimit))});
        $R->run(q{abline(v=0, lty=2, col="grey", lwd=1.5)});
        $R->run(q{plot(idata$relative_position,
                idata$norm_counts_no_copy_number_sense, type="o", main="Sense records
                (no copy number)", xlab="Relative position", ylab="Density",
                col="orange", ylim=c(0,ylimit))});
        $R->run(q{abline(v=0, lty=2, col="grey", lwd=1.5)});
        $R->run(q{plot(idata$relative_position,
                idata$norm_counts_with_copy_number_antisense, type="o",
                main="Anti-sense records (with copy number)", xlab="Relative
                position", ylab="Density", col="lightblue", ylim=c(0,ylimit))});
        $R->run(q{abline(v=0, lty=2, col="grey", lwd=1.5)});
        $R->run(q{plot(idata$relative_position,
                idata$norm_counts_no_copy_number_antisense, type="o", main="Anti-sense
                records (no copy number)", xlab="Relative position", ylab="Density",
                col="darkblue", ylim=c(0,ylimit))});
        $R->run(q{abline(v=0, lty=2, col="grey", lwd=1.5)});
        $R->run(q{graphics.off()});
        # Close R
        $R->stop();
}
1;