Aureliano Bombarely

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 <ab782@cornell.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.