Bio::Graphics::Glyph::pairplot - The "pairwise plot" glyph

Author

       Lincoln Stein <lstein@cshl.edu<gt>.

       Copyright (c) 2004 Cold Spring Harbor Laboratory

       This package and its accompanying libraries is free software; you can redistribute it and/or modify it
       under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic
       License 2.0.  Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.30.0                                       2019-11-25                Bio::Graphics::Glyph::pairplot(3pm)

Bugs

       Please report them.

Description

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

Name

       Bio::Graphics::Glyph::pairplot - The "pairwise plot" glyph

Synopsis

        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);
        }