/ 
R-YapRI-0.09
River stage zero No dependents
/ R::YapRI

NAME

R::YapRI - Yet Another Perl R Inteface

SYNOPSIS

 use R::YapRI::Base;

 ## WORKING WITH THE DEFAULT MODE:

 my $rbase = R::YapRI::Base->new();
 $rbase->add_command('bmp(filename="myfile.bmp", width=600, height=800)');
 $rbase->add_command('dev.list()');
 $rbase->add_command('plot(c(1, 5, 10), type = "l")');
 $rbase->add_command('dev.off()');

 $rbase->run_commands();
 
 my $result_file = $rbase->get_result_file();
 
 ## To work with blocks, check R::YapRI::Block

DESCRIPTION

Yet another perl wrapper to interact with R. R::YapRI is a collection of modules to interact with R using Perl.

The mechanism is simple, it writes R commands into a command file and execute it using the R as command line:

R [options] < infile > outfile

More information about the basic usage can be found in R::YapRI::Base.

But there are some tricks. It can also define blocks and combine them, so it can extend the interaction between packages of information. For example, it can create a block to check the length of a vector using default as base

my $newblock = $rbase->create_block('lengthblock', 'default');
$newblock->add_command('length(x * y)');
$newblock->run_block();
my @results = $newblock->read_results();

if ($results[0] == 10) {
   my $newblock2 = $rbase->create_block('meanblock', 'default');
   $newblock2->add_command('z <- mean(x * y)');
   $newblock2->run_block();
   my @results2 = $newblock2->read_results();
}

More information about the use of blocks can be found at R::YapRI::Block.

It can use interpreters (R::YapRI::Interpreter::Perl), so sometimes it can use perl HASHREF instead of strings to add_command.

$rbase->add_command('mean(c(2,3,5,7,11,13,17,19,23,29))');
$rbase->add_command({ mean => [2,3,5,7,11,13,17,19,23,29]});

It uses two switches to trace the R commands that you are running:

  • disable_keepfiles/enable_keepfiles, to not delete the command files and the result files after the execution of the code.

  • disable_debug/enable_debug, to print to STDERR the R commands from the command file before executing them.

ADVANCED FEATURES

Here are some examples of modules that wrap R::YapRI::Base for an extended functionality.

Matrix manipulation R::YapRI::Data::Matrix

 use R::YapRI::Base;
 use R::YapRI::Data::Matrix;

 my $rbase = R::YapRI::Base->new();
 $rbase->create_block('BLOCK1');

 my $rmatrix = R::YapRI::Data::Matrix->new( { name     => 'matrix1',
                                              coln     => 3,
                                              rown     => 3,
                                              colnames => ['a', 'b', 'c'],
                                              rownames => ['X', 'Y', 'Z'],
                                              data     => [1,2,3,4,5,6,7,8,9],
                                            } );

 $rmatrix->send_rbase($rbase, 'BLOCK1');
 $rbase->add_command('eigenvect1 <- eigen(matrix1)$vectors', 'BLOCK1');
 my $eigenvectors = read_rbase($rbase, 'BLOCK1', 'eigenvect1');

Simple graph creation R::YapRI::Graph::Simple

use R::YapRI::Base;
use R::YapRI::Data::Matrix;
use R::YapRI::Graph::Simple;

my $rbase = R::YapRI::Base->new();

my $rmatrix = R::YapRI::Data::Matrix->new( { name     => 'gene_expr',
                                             coln     => 2,
                                             rown     => 1,
                                             colnames => ['WT', 'Mut'],
                                             rownames => ['TIR1'],
                                             data     => [674, 54],
                                           } );

my $rgraph = R::YapRI::Graph::Simple->new({
  rbase  => $rbase,
  rdata  => { height => $rmatrix },
  grfile => "TirGeneExpression.bmp",
  device => { bmp => { width => 600, height => 600 } },
  sgraph => { barplot => { beside => 'TRUE',
                           main   => 'Tir Gene Expression',
                           xlab   => 'Samples',
                           ylab   => 'Expression',
                           col    => ["dark blue", "dark red"],
            } 
  },

$rgraph->build_graph('GRAPHBLOCK1');
my ($filegraph, $fileresults) = $rgraph->build_graph();

AUTHOR

Aureliano Bombarely <aurebg@vt.edu>

ACKNOWLEDGEMENTS

  • Lukas Mueller

  • Robert Buels

  • Naama Menda

  • Jonathan "Duke" Leto

  • Olivier "dolmen" Mengué

PUBLIC REPOSITORY

Hosted at GitHub: https://github.com/solgenomics/yapri

COPYRIGHT AND LICENCE

Copyright 2011 Boyce Thompson Institute for Plant Research

Copyright 2011 Sol Genomics Network (solgenomics.net)

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.