Summary

Bio::Graphics - Generate GD images of Bio::Seq objects

Package variables

Included modules

Synopsis

  use Bio::Graphics;
  use Ace::Sequence; # or any other way to create a Bio::Seq object

  # get a set of Bio::SeqFeature objects ... somehow
  my $db     = Ace->connect(-host=>'brie2.cshl.org',-port=>2005) or die;
  my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
				  -db=>$db,-start=>-15000,-end=>15000) or die;
  my @transcripts = $cosmid->transcripts;

  # let the drawing begin...
  my $panel = Bio::Graphics::Panel->new( -segment => $cosmid,
				         -width   => 800  );

  $panel->add_track(arrow => $cosmid,
 		    -bump => 0,
 		    -tick =>2);

  $panel->add_track(transcript => \@transcripts,
 		    -bgcolor   =>  'wheat',
 		    -fgcolor   =>  'black',
                    -key       => 'Curated Genes',
 		    -bump      =>  +1,
 		    -height    =>  10,
 		    -label     =>  1);

  my $boxes = $panel->boxes;
  print $panel->png;

Description

Please see Bio::Graphics::Panel for the full API.

Methods description

None available.

Methods code

No methods available.

General documentation

Bio::Graphics::Panel,
Bio::Graphics::Glyph,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
Bio::DB::GFF::Feature,
Ace::Sequence,
GD

Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.