The arrayref that needs to be passed to the plot() method is quite complex. It needs a reference to an array of array references (if you can get your head around that!). The first arrayref in @array contains the values for x that you want to plot y-values for. Each additional arrayref contains the y-values for one line. Like this:

open (FH, "<data.txt");

while (<FH>) {
chomp ($_);

($x, $y) = split (/\s+/, $_) unless /RT/;
   push @xes, $x;
   push @ys, $y;
}


my $mygraph = GD::Graph::lines->new(600, 300);
$mygraph->set(
x_label => 'RT',
y_label => 'HEIGHT',
title => 'xxx'
);

$image = $mygraph->plot( [ \@xes, \@ys ] ) or die $mygraph->error;

open(IMG, '>file2.png') or die $!;
binmode IMG;
print IMG $image->png;
close IMG;
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