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
[download]

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();
[download]

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.