Calling R codes from PERL using system coomand

[anikng]

Hi Members... I am in confusion that how to integrate R codes in PERL program using system command (not through any additional packages). Specifically my PERL code generate microarray data (in .csv format) and save the data in a file "array_data.csv". I wanted following R code to generate a microarray heatmap. I have attached R scrip to generate hetamap. I am working on Ubuntu 14.04 Desktop. Perl V 5.18. If someone can just show an example, it would be helpful for me. Thanks, anikng, ROK

 

>library(gplots)
>library(RColorBrewer)
>all.data <- read.csv("C:/Users/Anil/Desktop/sam.csv")
>row.names(all.data) <- all.data$sample
>all.data <- all.data[, -1]
>data.prop <- all.data/rowSums(all.data)
>scaleyellowred <- colorRampPalette(c("lightyellow", "red"), space = "
+rgb")(100)
>heatmap(as.matrix(data.prop), Rowv = NA, Colv = NA, col = scaleyellow
+red)

[AppleFritter]

Howdy anikng, and welcome to the Monastery!

I'm not familiar with R, but if you can't use non-core modules, this page suggests that you can invoke R like this to execute commands from a file:

R CMD BATCH /path/to/file.R

Alternatively, there is a module, Statistics::R, to interface R with Perl. So if installing that is an option, you could also do this:

use Statistics::R;
  
my $R = Statistics::R->new();
my $csvfile = "C:/Users/Anil/Desktop/sam.csv";

my @R_commands = (
    'library(gplots)',
    'library(RColorBrewer)',
    "all.data <- read.csv($csvfile)",
    'row.names(all.data) <- all.data$sample'
    'all.data <- all.data[, -1]'
    'data.prop <- all.data/rowSums(all.data)',
    'scaleyellowred <- colorRampPalette(c("lightyellow", "red"), space
+ = "rgb")(100)',
    'heatmap(as.matrix(data.prop), Rowv = NA, Colv = NA, col = scaleye
+llowred)'
);

$R->run(@R_commands);
$R->stop();

Totally untested, though.

There's also a ->run_from_file() method if you'd rather read commands from an external file than embedding them in your Perl script.

[anikng]

Thank u very much AppleFritter.. I will go on with Statistics::R. Your code gave me the idea!!! anikng, ROK

[Anonymous Monk]

not through any additional packages

You can install modules even if you're not an administrator / root, see for example local::lib. (Sometimes, there are legitimate reasons for not being able to use a module, but those are rare!) You really should try to install modules that will help you, such as Statistics::R from AppleFritter's answer.

Running external commands is easier via helper modules, my two go-to modules are IPC::System::Simple as a drop-in replacement for system or IPC::Run3 for manipulating STDIN, STDOUT and STDERR.

Having said that, how to use system is explained in its documentation. In your case it would look something like this (untested):

system("R", "CMD", "BATCH", $R_FILENAME) == 0
    or die "calling R failed: $?";