[Bioperl-l] Problems with Bioperl graphics

[Crabtree, Jonathan]

One difference between your code and the tutorial is that you've set
-label to 4 in your call to add_track(); in the tutorial this parameter
is set to 1.  Try changing the 4 to 1 and see what happens.  Another
difference is that you're using the 'graded_segments' glyph instead of
the 'generic' glyph (I don't think this should matter, but you were
asking whether your code differs from that in the tutorial ;)

Jonathan


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Wacki
> Sent: Tuesday, July 05, 2005 3:23 AM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Problems with Bioperl graphics
> 
> 
> I followed the tutorial here:
> 
> http://bioperl.org/HOWTOs/Graphics-HOWTO/gettingStarted.html
> 
> And ran this exact code:
> 
> http://biokdd.informatics.indiana.edu/jnowacki/render_blast1.txt
> 
> The image produced is shown here:
> 
> http://biokdd.informatics.indiana.edu/jnowacki/test.png
> 
> It doesn't have the name of the hits.  What is wrong?  The 
> code is exactly the same as the tutorial is it not?
> 
> 
> 
> 
> 
> 
> code:
> 
> #!/usr/bin/perl
> 
> # This is code example 2 in the Graphics-HOWTO
> use strict;
> use lib '/home/lstein/projects/bioperl-live';
> use Bio::Graphics;
> use Bio::SeqFeature::Generic;
> 
> my $panel = Bio::Graphics::Panel->new(-length => 1000,
>                                       -width  => 800,
>                                       -pad_left => 10,
>                                       -pad_right => 10,
>                                       );
> my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>1000);
> $panel->add_track($full_length,
>                   -glyph   => 'arrow',
>                   -tick    => 2,
>                   -fgcolor => 'black',
>                   -double  => 1,
>                   );
> 
> my $track = $panel->add_track(-glyph => 'graded_segments',
>                               -label  => 4,
>                               -bgcolor => 'blue',
>                               -min_score => 0,
>                               -max_score => 1000);
> 
> while (<>) { # read blast file
> chomp;
> next if /^\#/;  # ignore comments
> my($name,$score,$start,$end) = split /\t+/;
> my $feature = 
> Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,
>                                             
> -start=>$start,-end=>$end); $track->add_feature($feature); }
> 
> binmode(STDOUT);
> print $panel->png;
> 
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