I couldn't see how to do stacked bars with Chart::Gnuplot. This example uses GD::Graph.

#!perl
use strict;
use GD;
use GD::Graph::bars;
use GD::Graph::hbars;

# read header for y legend
chomp( my $header = <DATA> );
my (undef,@y_legend) = split /\s+/,$header;

# read rows of data
my @data=();
while (<DATA>){
  chomp;
  my @col = split /\s+/,$_;
  for my $i (0..$#col){
    push @{$data[$i]},$col[$i];
  }  
}

# create vertical stacked bars graph
# use hbars->new for horiz stacked bars
my $my_graph = GD::Graph::bars->new(1000,500);
$my_graph->set(
  x_label => 'Method',
  y_label => 'Y label',
  title => 'Stacked Bar',
  cumulate => 2,
  bar_spacing => 5,
  transparent => 0,
);
# Allowed 
# white, lgray, gray, dgray, black, lblue, blue, dblue, gold, lyellow,
+ yellow, 
# dyellow, lgreen, green, dgreen, lred, red, dred, lpurple, purple, dp
+urple, lorange, 
# orange, pink, dpink, marine, cyan, lbrown, dbrown.

my @colour_array = qw(lblue dbrown blue  lred   lgreen yellow
                      green red   purple orange pink   dyellow);
$my_graph->set( dclrs => \@colour_array );

# text sizes
# gdGiantFont, gdLargeFont, gdMediumBoldFont, gdSmallFont , gdTinyFont
$my_graph->set_x_label_font(gdGiantFont);
$my_graph->set_x_axis_font(gdSmallFont);
$my_graph->set_y_label_font(gdGiantFont);
$my_graph->set_y_axis_font(gdMediumBoldFont);
$my_graph->set_title_font(gdGiantFont);
$my_graph->set_legend_font(gdGiantFont);
$my_graph->set_legend( @y_legend );

# plot
my $img = $my_graph->plot(\@data);

# save
open(IMG, '>file.png') or die $!;
binmode IMG;
print IMG $img->png;

__DATA__
METHOD    0TM    1TM    2TM    >2TM
method1    3    68    18    10
method2    3    80    10    6
method3    3    87    9    1
method4    5    83    9    3
method5    6    75    15    4
method6    14    77    6    3
method7    12    82    2    3
method8    9    84    3    3
method9    13    68    16    3
method10    5    65    20    9
method11    9    64    20    7
method12    5    68    18    9
method13    6    82    9    2
method14    11    79    8    2
method15    6    69    20    5
method16    5    80    11    3
method17    1    68    17    14
[download]

Thank you a lot for all your trouble!

I am almost there with Chart::Gnuplot.
One question still remains to be answered...
In the final step, the:


$chart->plot2d($h1, $h2, $h3...)
[download]


where $h1, $h2, $h3 etc are the various datasets created with Chart::Gnuplot::DataSet->new, how can I pass the names ($h1, $h2 etc) if I have them in an array?
My final version of the code so far is:

#!/usr/bin/perl
use Chart::Gnuplot; 

#one must specify FILENAME to get data from (tab-delimited), a name fo
+r the output file, a type for output file (e.g. pdf, png, eps) and a 
+plot title
($infile, $title, $type, $plot_title) = @ARGV;
$outfile = $title.'.'.$type;

#add or remove colours accordingly    
@colour_array = ("lblue", "brown", "blue", "lred", "lgreen", "yellow",
+ "green", "red", "purple", "orange", "pink", "dyellow");

@data;
$counter;

open IN, "$infile" or die $!; 
$label_line = <IN>; chomp $label_line;    #find the labels data (for n
+aming the colours in the stacked bars)
@split_labels = split(/\t/, $label_line);

while(<IN>)
{
    chomp; 
      $counter = 0;
      for (split/\t/,$_)
    { push @{$data[$counter++]}, $_; }
}
close IN;

#x-axis labels is the row #0 in the AoA @data
@x = @{$data[0]};

$total_y = @data-1;    #find how many y rows we have => how many colou
+rs we need (-1 because #0 is x-axis)
@pick_colours = @colour_array[ 0 .. $total_y - 1 ];

# Initiate the chart object 
$chart = Chart::Gnuplot->new( 
    output => $outfile, 
    title => $title, 
    xlabel => { 
            text => 'Method', 
            color => 'black',
            offset => "-1",
            font => 'Times-Roman, 20'
          },
    ylabel => { 
            text => $plot_title, 
            color => 'black',
            offset => -1,
            font => 'Times-Roman, 20'
          },
    yrange => [0, '*'], 
    xtics => { rotate => '-270', font => 'Times-Roman, 15' },    
    ytics => { font => 'Times-Roman, 15' },    
    bg => {
            color   => 'white',
            density => 0.2,
          },
    plotbg => 'white',
    legend => {position => 'outside bottom'}, 
    border => {
                sides    => 'bottom, left',
                linetype => 3,
                width    => 2,
                color    => 'black',
          },

    "style histogram" => 'rowstacked'
); 

#all the rest rows in @data are used for creating the histogram bars
#create object foreach series of data (column in excel)
$counter_objects=0;
@all_vars=();
for $y ( 1 .. $#data ) 
{
    $legend_name = $split_labels[$y];    #get the name for the legend,
+ e.g 1TM, 2TM, >2TM
    @tmp_y = @{$data[$y]};            #create temp array


    $counter_objects++;
    
    $myvar.= '$h'."$counter_objects".", "; 
    push @all_vars, $myvar;
    ${h."$counter_objects"} = Chart::Gnuplot::DataSet->new
    ( 
        xdata => \@x, 
        ydata => \@tmp_y, 
        title => "$legend_name", 
        fill => {density => 0.2}, 
        style => "histograms", 
    ); 
}

$wanted = substr ($string_of_vars,0, -2); 

$chart->plot2d(\@all_vars);
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but in the last step, it complaints, because:


Not a HASH reference at /usr/local/share/perl/5.14.2/Chart/Gnuplot.pm
[download]