Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Generate GD images of biological sequences and annotations
Perl

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
Graphics
eg
Changes
DISCLAIMER.txt
MANIFEST
Makefile.PL
README
test.pl

README

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

SYNOPSIS

  use Ace::Sequence;  # or any Bio::Seq factory
  use Bio::Graphics::Panel;

  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;

  my $panel = Ace::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

The Bio::Graphics::Panel class provides drawing and formatting
services for any object that implements the Bio::SeqFeatureI
interface, including Ace::Sequence::Feature and Das::Segment::Feature
objects.  It can be used to draw sequence annotations, physical
(contig) maps, or any other type of map in which a set of discrete
ranges need to be laid out on the number line.

The module supports a drawing style in which each type of feature
occupies a discrete "track" that spans the width of the display.  Each
track will have its own distinctive "glyph", a configurable graphical
representation of the feature.

The module also supports a more flexible style in which several
different feature types and their associated glyphs can occupy the
same track.  The choice of glyph is under run-time control.

Semantic zooming (for instance, changing the type of glyph depending
on the density of features) is supported by a callback system for
configuration variables.  The module has built-in support for Bio::Das
stylesheets, and stylesheet-driven configuration can be intermixed
with semantic zooming, if desired.

You can add a key to the generated image using either of two key
styles.  One style places the key captions at the top of each track.
The other style generates a graphical key at the bottom of the image.

Note that this modules depends on GD.
Something went wrong with that request. Please try again.