Bio::Graphics::Glyph::pairplot(3pm)

Usage

 use Bio::Graphics;
 # create the panel, etc.  See Bio::Graphics::Panel
 # for the synopsis
 # Create one big feature using the PairFeature
 # glyph (see end of synopsis for an implementation)
 my $block = PairFeature->new(-start=>  2001,
                              -end  => 10000);
 # It will contain a series of subfeatures.
 my $start = 2001;
 while ($start < 10000) {
   my $end = $start+120;
   $block->add_SeqFeature($bsg->new(-start=>$start,
                                    -end  =>$end
                                   ),'EXPAND');
   $start += 200;
 }
 $panel->add_track($block,
                   -glyph => 'pairplot',
                   -angle => 45,
                   -bgcolor => 'red',
                   -point => 1,
                  );
 print $panel->png;
 package PairFeature;
 use base 'Bio::SeqFeature::Generic';
 sub pair_score {
   my $self = shift;
   my ($sf1,$sf2) = @_;
   # simple distance function
   my $dist  = $sf2->end    - $sf1->start;
   my $total = $self->end   - $self->start;
   return sprintf('%2.2f',1-$dist/$total);
 }

Overview

This glyph draws a "triangle plot" similar to the ones used to show linkage disequilibrium between a series of genetic markers. It is basically a dotplot drawn at a 45 degree angle, with each diamond-shaped region colored with an intensity proportional to an arbitrary scoring value relating one feature to another (typically a D' value in LD studies).

This glyph requires more preparation than other glyphs. First, you must create a subclass of Bio::SeqFeature::Generic (or Bio::Graphics::Feature, if you prefer) that has a pair_score() method. The pair_score() method will take two features and return a numeric value between 0.0 and 1.0, where higher values mean more intense.

You should then create a feature of this new type and use add_SeqFeature() to add to it all the genomic features that you wish to compare.

Then add this feature to a track using the pairplot glyph. When the glyph renders the feature, it will interrogate the pair_score() method for each pair of subfeatures.

Options

In addition to the common options, the following glyph-specific options are recognized:

  Option      Description                  Default
  ------      -----------                  -------
  -point      If true, the plot will be         0
              drawn relative to the
              midpoint between each adjacent
              subfeature.  This is appropriate
              for point-like subfeatures, such
              as SNPs.
  -angle      Angle to draw the plot.  Values   45
              between 1 degree and 89 degrees
              are valid.  Higher angles give
              a more vertical plot.
  -bgcolor    The color of the plot.            cyan

Releases

8 releases since Debian 6.0 (Squeeze); the text changed 5 times.

6.0
7
8
9
10
11–13