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lib/CLIPSeqTools/PlotApp/conservation_distribution.pm  view on Meta::CPAN

=head1 NAME

CLIPSeqTools::PlotApp::conservation_distribution - Create plots for script
conservation_distribution.

=head1 SYNOPSIS

clipseqtools-plot conservation_distribution [options/parameters]

=head1 DESCRIPTION

Create plots for script conservation_distribution.

=head1 OPTIONS

  Input.
    --file <Str>                 file with conservation distribution.

  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::conservation_distribution;
$CLIPSeqTools::PlotApp::conservation_distribution::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 => 'file with conservation distribution.',
);

#######################################################################
##########################   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 for conservation with R\n" if $self->verbose;
	$self->run_R;
}

sub run_R {
	my ($self) = @_;

	my $figfile = $self->o_prefix . 'conservation_distribution.pdf';

	# Start R
	my $R = Statistics::R->new();

	# Pass arguments to R
	$R->set('ifile', $self->file);
	$R->set('figfile', $figfile);

	# Disable scientific notation
	$R->run(q{options(scipen=999)});