GD::Graph is basically a bunch of special purpose drawing primitives for GD, which just draws pixels onto a bitmap. In other words, if you ask GD::Graph to put a bar 5 units high at point 7 of the Y axis, it will push pixels to do exactly that, regardless of what pixels where there before.

With that in mind, I think you need to process your data a bit more before you plot it.

No I can't sort the data first as it is being used on a bar chart where the x-axis is the date. Some sort of sort needs to actually go on within GD::Graph to sort the columns before drawing them.

use GD::Graph::lines;
use GD::Graph::bars;

$suffix = @ARGV[0]; #Suffix
$accur = @ARGV[1]; #Accuracy
$mode = @ARGV[2]; #Mode (se - start/end or fd - full day)
if ($accur eq "" || $suffix eq ""){print "Usage: perl WAC.pl [suffix] 
+[hour minute] <fd se>"; exit;}

($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time
+);
$year = $year+1900;

$hour = sprintf("%.2d",$hour);
$min = sprintf("%.2d",$min);
$sec = sprintf("%.2d",$sec);

@plot_legend = ('Exceptions','Successes','WAC_002','Errors');

&check_usage();
&read_data();
&date_setup();
&date_hash();
&parse_data();
&plot_prepare();
&plot_graph();

print "Graph OK\n";

sub plot_prepare(){
    foreach (sort(keys %date_plots)){        
        push(@plots_date,$_);
        push(@plots_exception,$exception{$_});
        push(@plots_success,$success{$_});
        push(@plots_wac,$wac{$_});
        push(@plots_error,$error{$_});
        #print "$_ -> $success{$_}\n";
    }
}

sub parse_data(){
    my %line;
    foreach (@data){
        chomp($_);
        %line = &return_data($_);
        #print "$line{date_string}\n";
        if ($l_msg =~ "Exception"){$exception{$line{date_string}} = $l
+ine{l_count};}
        if ($l_msg =~ "Success"){$success{$line{date_string}} = $line{
+l_count};}
        if ($l_msg =~ "wac_002"){$wac{$line{date_string}} = $line{l_co
+unt};}
        if ($l_msg =~ "Errorcode" && $l_msg !~ "wac_002"){$error{$line
+{date_string}} = $line{l_count};}
    }
}

sub date_setup(){
    %d_first = &return_data(@data[0]);
    %d_last = &return_data(@data[$#data]);

    print "First date: $d_first{month}/$d_first{day} $d_first{hour}:$d
+_first{min}\n";
    print "Last date: $d_last{month}/$d_last{day} $d_last{hour}:$d_las
+t{min}\n";
}

sub date_hash(){
    print "Accuracy is $accur\n";
    my $l_min,$l_hr,$l_mon,$l_day;
    my $t_min,$t_hr,$t_mon,$t_day;
    
    $t_mon = sprintf("%.2d",$d_first{month});
    $t_day = $d_first{day};
    
    if ($mode eq "fd"){
        $t_hr = 0;
        $t_min = 0;
    }
    else{
        $t_hr = $d_first{hour};
        $t_min = $d_first{min};
    }
    
    $l_date_min = sprintf("%.2d", $l_date_min);
    $l_date_hr = sprintf("%.2d", $l_date_hr);
    $l_date_day = sprintf("%.2d", $l_date_day);
    $l_date_month = sprintf("%.2d", $l_date_month);
    
    while ($t_mon <= $d_last{month}){
        while ($t_day <= $d_last{day} || ($t_mon < $d_last{month} && $
+t_day <= 31)){
            while ($t_hr <= 23){
                if ($accur eq "minute"){
                    while ($t_min <= 59){
                      unless ($t_day eq $d_last{day} && $t_hr > $d_las
+t{hour} && $mode ne "fd"){
                        unless ( ($t_min > $d_last{min} && $t_hr >= $d
+_last{hour}) && $mode ne "fd"){
                            #print "Add:" . sprintf("%.2d",$t_mon). "/
+" . sprintf("%.2d",$t_day) . " " . sprintf("%.2d",$t_hr) . ":" . spri
+ntf("%.2d",$t_min) . "\n";
                            $date_plots{sprintf("%.2d",$t_mon). "/" . 
+sprintf("%.2d",$t_day) . " " . sprintf("%.2d",$t_hr) . ":" . sprintf(
+"%.2d",$t_min)}=0;
                        }
                      }
                      $t_min++;
                    }
                    $t_min = 0
                }elsif($accur eq "hour"){
                    unless ($t_day eq $d_last{day} && $t_hr > $d_last{
+hour}){
                        $date_plots{sprintf("%.2d",$t_mon). "/" . spri
+ntf("%.2d",$t_day) . " " . sprintf("%.2d",$t_hr) . ":00"}=0;
                    }
                }
                $t_hr++;
                $t_min = 0;
            }
            $t_hr = 0;
            $t_day++;
        }
        $t_mon++;
        $t_day = 1;
    }
}

sub check_usage(){
    if ($accur eq "" || $suffix eq ""){
        print "Usage: perl WAC.pl [suffix] [hour minute]";
        exit;
    }
}

sub read_data(){
    print "Reading...\n";
    open(HANDLE,"./$suffix\_$accur.txt") || die $!;
    @data = <HANDLE>;
    close(HANDLE);
}

sub return_data(){
    my $line = $_[0];
    my $date;
    my $return_hash;
    
    #print "$line\n";
    
    ($l_date,$l_count,$l_msg) = split(/\t/,$line);
    ($l_date_a,$l_date_b,$date_c) = split(/ /,$l_date);
    ($l_date_month,$l_date_day,$extra_date) = split(/\//,$l_date_a);
    ($l_date_hr,$l_date_min,$extra_time) = split(/\:/,$l_date_b);
    
    if ($l_date_hr eq ""){$l_date_hr = "00";}
    if ($l_date_min eq ""){$l_date_min = "00";}
    
    if ($date_c eq "PM" && $l_date_hr != 12){$l_date_hr += 12;}
    
    $l_date_min = sprintf("%.2d", $l_date_min);
    $l_date_hr = sprintf("%.2d", $l_date_hr);
    $l_date_day = sprintf("%.2d", $l_date_day);
    $l_date_month = sprintf("%.2d", $l_date_month);
    
    $return_hash{l_count} = $l_count;
    $return_hash{l_msg} = $l_msg;
    $return_hash{month} = $l_date_month;
    $return_hash{day} = $l_date_day;
    $return_hash{hour} = $l_date_hr;
    $return_hash{min} = $l_date_min;
    $return_hash{date_string} = "$l_date_month/$l_date_day $l_date_hr:
+$l_date_min";
    
    return %return_hash;
}

sub plot_graph(){
    @data = (
            \@plots_date,
            \@plots_exception,  #Red
            \@plots_success, #Green
            \@plots_wac,  #Yellow
            \@plots_error,  #?
         );

    my $graph = GD::Graph::bars->new(1000,700);
      $graph->set(
          correct_width => 0,
          x_label           => 'Days',
          y_label           => 'WAC service response',
          title             => "WAC Service Call Results as of: $mon/$
+mday/$year $hour:$min:$sec",
          t_margin => 10,
          b_margin => 10,
          l_margin => 10,
          r_margin => 100,
          #x_label_skip => sprintf("%.0d",$#plots_date / 12),
          show_values => 0,
          x_label_position => 0.50,
          y_label_position => 0.50,
          x_labels_vertical => 1,
          y_long_ticks => 1,
          #line_types => [1,1,1],
          #skip_undef => 1,
          boxclr => 'white',
          fgclr => 'gray',
          #bar_width => 1,
          accent_treshold => 1,
          #cumulate => 1,
          #show_values => 1,
          overwrite => 1,
          axislabelclr => 'black',
          dclrs => [ qw(red green blue orange) ]
          
      ) or die $graph->error;
      
      $graph->set_text_clr('black');
      
      if ($accur eq "hour"){
        print $#plots_date;
        if ($#plots_date == 24){$graph->set(x_label_skip=>1);}
        elsif ($#plots_date <= 200){$graph->set(x_label_skip=>8);}
        else{$graph->set(x_label_skip=>64);}
      }
      if ($accur eq "minute"){
        $graph->set(x_label_skip=>$#plots_date/24);
      }
      
      $graph->set_legend(@plot_legend);
      $graph->set_legend_font(GD::gdMediumBoldFont);
      $graph->set_title_font(GD::gdMediumBoldFont);
      
      my $gd = $graph->plot(\@data) or die $graph->error;
    
      open(IMG, ">./$suffix\_$accur.png") or die $!;
      binmode IMG;
      print IMG $gd->png;
}
[download]

Is it possible to sort the values by size before passing them to the graphing code?

That is exactly how I solved this problem in the past.

My code is posted above, if you know a way of sorting the order for each bar to be drawn for each time period please let me know