Hello I am new to perl monks and I am using GD::Graph::lines to create a plot but for some reason I am getting an error "Invalid data set: 0". I can't seem to figure out the reason why I am getting this error. Below is my code, I know there are some initialized variables which haven't been used yet. I am working on creating the graph for "R1". Once that works I'll just copy and paste to create it for "R2"

#!/usr/bin/perl -w                                                    
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+                                                                 

use strict;
use warnings;
use Data::Dumper;
use Cwd;
use GD::Graph::lines;
use GD::Graph::colour;
GD::Graph::lines->import();
GD::Graph::colour->import(qw(:colours :lists :files :convert));

my $dir = getcwd();
my $meth = 0;
my $unmeth = 0;
my $meth_perc = 0;
my @data_R1 = ();
my @data_R2 = ();
my %sum_R1 = ();
my %sum_R2 = ();
my $tmp = $ENV{TMP};
my @graph_R1 = ();
my @graph_R2 = ();

#print $tmp."\n";                                                     
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opendir(DIR,$dir) or die "Cannot open directory path $dir\n";
my @mbias = grep(/\.M-bias.txt$/,readdir(DIR));
closedir(DIR);

for(my $i=0;$i<scalar(@mbias);$i++){

    open (FILE,$mbias[$i]) or die "Could not open: $!";
    open (IN,">".$tmp.($i+1)."_R1.txt") or die "Could not write to: $!
+";
    while (<FILE>) {
        push @data_R1, $_ if (/^CpG context \Q(R1)/ .. /^125/);
    }
    for(my $j=3;$j<scalar(@data_R1);$j++){
        print IN $data_R1[$j];
    }
    close (IN);
    @data_R1 = ();
}

opendir(TMP,$tmp) or die "Cannot open directory path $tmp\n";
my @R1 = grep(/\_R1.txt$/,readdir(TMP));

for(my $i=0;$i<125;$i++){

    push (@{$sum_R1{$i+1}},($i+1),0,0,0);

}

for(my $i=0;$i<scalar(@R1);$i++){

    open(FILE,$tmp."$R1[$i]") or die "Could not open: $!";
    my @file = <FILE>;
    chomp @file;

    foreach my $key(keys %sum_R1){

        for(my $j=0;$j<scalar(@file);$j++){
            my @split = split("\t",$file[$j]);
            $meth = $split[1];
            $unmeth = $split[2];

            if($key == $split[0]){
                @{$sum_R1{$key}}[1] += $meth;
                @{$sum_R1{$key}}[2] += $unmeth;

            }
        }
        $meth=0;
        $unmeth=0;
    }
    close (FILE);
}

foreach my $key(keys  %sum_R1){

    $meth = @{$sum_R1{$key}}[1];
    $unmeth = @{$sum_R1{$key}}[2];
    $meth_perc = 100*($meth/($meth + $unmeth));
    @{$sum_R1{$key}}[3] = $meth_perc;
}

foreach my $key(sort {$a <=> $b} keys %sum_R1){

    push @graph_R1, @{$sum_R1{$key}}[3];

}

my $graph1 = GD::Graph::lines->new(800,600);

add_colour(nice_blue => [31,120,180]);

$graph1->set(
                 x_label              => 'position (bp)',
                 y1_label              => '% methylation',
                 y2_label              => '# methylation calls',
                 title                => 'Mbias plot Read 1',
                 line_width           => 2,
                 x_max_value          => 125,
                 x_min_value          => 0,
                 y_tick_number        => 10,
                 y_label_skip         => 2,
                 y1_max_value          => 100,
                 y1_min_value          => 0,
                 y_label_skip         => 2,
                 y2_min_value          => 0,
                 x_label_skip         => 5,
                 x_label_position     => 0.5,
                 x_tick_offset        => -1,
                 bgclr                => 'white',
                 transparent          => 0,
                 two_axes             => 1,
                 use_axis             => [1,1,1,2,2,2],
                 legend_placement     => 'RC',
                 legend_spacing       => 6,
                 legend_marker_width  => 24,
                 legend_marker_height => 18,
                 dclrs              => [ qw(nice_blue) ],
    )or die $graph1->error;

$graph1->set_legend('CpG methylation');

my $gd = $graph1->plot(\@graph_R1) or die $graph1->error;

open(IMG, '>test.png') or die $!;
binmode IMG;
print IMG $graph1->png;

[download]

I hope I was thorough enough in explaining my problem. Thanks in advance.

In reply to GD graph Invalid data set by sramazan

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