NAME
R::YapRI::Interpreter.pm
A module to transform perl variables into R command lines to define simple objs.
SYNOPSIS
use R::YapRI::Base;
use R::YapRI::Interpreter::Perl qw/r_var/;
my $perl_var = [1, 2, 3];
my $r_var = r_var($perl_var); DESCRIPTION
A interpreter to translate Perl variables into R commands for R::YapRI::Base
+==================+==============+===============================+
| PERL VARIABLE | R VARIABLE | Example |
+==================+==============+===============+===============+
| undef | NULL | $px = undef | rx <- NULL |
+------------------+--------------+---------------+---------------+
| empty ('' or "") | NA | $px = '' | rx <- NA |
+------------------+--------------+---------------+---------------+
| integer | numeric | $px = 12 | rx <- 12 |
+------------------+--------------+---------------+---------------+
| bigint,bigfloat | numeric | $px = '-1.2' | rx <- -1.2 |
+------------------+--------------+---------------+---------------+
| word 'TRUE' | TRUE | $px = 'TRUE' | rx <- TRUE |
+------------------+--------------+---------------+---------------+
| word 'FALSE' | FALSE | $px = 'FALSE' | rx <- FALSE |
+------------------+--------------+---------------+---------------+
| any other word | character | $px = "sun" | rx <- "sun" |
+------------------+--------------+---------------+---------------+
| ARRAY REF. | vector | $px = [1, 2] | rx <- c(1, 2) |
+------------------+--------------+---------------+---------------+
| HASH REF. | object | see below (*) |
+------------------+--------------+-------------------------------+
* R object or R function without arguments
$px = { a => undef }, will be just 'a'
$px = { mass => '' }, will be just 'mass'* R simple object with arguments
$px = { '' => { x => 2 }}, will be 'x = 2'
$px = { '' => { x => [2, 4] }}, will be 'x = c(2, 4)* R functions with arguments
$px = { log => 2 }, will be 'log(2)'
$px = { log => [2, { base => 10 }] }, will be 'log(2, base = 10 )'
$px = { t => {x => ''} }, will be 't(x)'
$px = { plot => [{ x => ''}, { main => "TEST"} ]}, will be:
plot(x, main = "TEST")Use array ref. to order the arguments in a function.
Use hash ref keys to define an argument in an R function
For more complex data structures, use R::YapRI::Data::Matrix.
AUTHOR
Aureliano Bombarely <aurebg@vt.edu>
CLASS METHODS
The following class methods are implemented:
_rvar_noref
Usage: my $r_string = _r_var_noref($perl_var);
Desc: Internal function to parse a single non-reference perl variable
(scalar). Equivalence table:
+==================+==============+=============================+
| PERL VARIABLE | R VARIABLE | Example |
+==================+==============+===============+=============+
| undef | NULL | $px = undef | rx <- NULL |
+------------------+--------------+---------------+-------------+
| empty ('' or "") | NA | $px = '' | rx <- NA |
+------------------+--------------+---------------+-------------+
| integer | numeric | $px = 12 | rx <- 12 |
+------------------+--------------+---------------+-------------+
| bigint,bigfloat | numeric | $px = '-1.2' | rx <- -1.2 |
+------------------+--------------+---------------+-------------+
| word 'TRUE' | TRUE | $px = 'TRUE' | rx <- TRUE |
+------------------+--------------+---------------+-------------+
| word 'FALSE' | FALSE | $px = 'FALSE' | rx <- FALSE |
+------------------+--------------+---------------+-------------+
| any other word | character | $px = "sun" | rx <- "sun" |
+------------------+--------------+---------------+-------------+
Ret: $r_string, a scalar with the perl2R variable translation
Args: $perl_var, could be, a scalar or an array reference
Side_Effects: Die if is used a perl reference.
Example: my $rvar = _rvar_noref(12);_rvar_vector
Usage: my $r_arg = _rvar_vector($arrayref);
Desc: Internal function to convert an perl array into a R vector
Ret: $r_arg, a scalar with the perl2R variable translation
Args: $arrayref, with the argument list
Side_Effects: Die if the argument is not an arrayref.
Example: my $r_vector = _rvar_vector($arrayref);_rvar_arg
Usage: my $r_arg = _rvar_arg($hashref);
Desc: Internal function to convert an argument in a function in the following
way:
2 ===> '2'
'YES' ===> '"YES"'
[2, 3] ===> 'c(2, 3)'
{ x => undef } ===> 'x'
{ type => "p" } ===> 'type = "p"'
{ col => ["blue", "green"]} ===> 'col = c("blue", "green")'
{ labels => { x => undef } } ===> 'labels = x'
Something different from that, will die.
Ret: $r_arg, a scalar with the perl2R variable translation
Args: $hashref, with the argument list
Side_Effects: Die if the argument is not: scalar, array ref or a hash
reference.
Example: my $arg = _rvar_arg({ type => "p" });r_var
Usage: my $r_string = r_var($perl_var);
Desc: Parse a perl variable and return a string with the r variable format,
For perl-non reference variables, see _rvar_noref
+==================+=================+==============================+
| PERL VARIABLE | R VARIABLE | Example |
+==================+=================+==============+===============+
| ARRAY REF. | vector | $px = [1, 2] | rx <- c(1, 2) |
+------------------+-----------------+--------------+---------------+
| HASH REF. | object/function | see below |
+------------------+-----------------+------------------------------+
* R object or R function without arguments
$px = { a => undef }, will be just 'a'
$px = { mass => '' }, will be just 'mass'
* R simple object with arguments
$px = { '' => { x => 2 }}, will be 'x = 2'
$px = { '' => { x => [2, 4] }}, will be 'x = c(2, 4)
* R functions with arguments
$px = { log => 2 }, will be 'log(2)'
$px = { log => [2, { base => 10 }] }, will be 'log(2, base = 10 )'
$px = { t => {x => ''} }, will be 't(x)'
$px = { plot => [{ x => ''}, { main => "TEST"} ]}, will be:
plot(x, main = "TEST")
Use array ref. to order the arguments in a function.
Use hash ref keys to define an argument in an R function
Ret: $r_string, a scalar with the perl2R variable translation
Args: $perl_var, could be, a scalar or an array reference
Side_Effects: Die if the reference used is not a ARRAY REF or HASH REF.
Example: my $rvar = r_var([1, 2, 3, "TRUE", "last word"]);ACKNOWLEDGEMENTS
Lukas Mueller
Robert Buels
Naama Menda
Jonathan "Duke" Leto
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.