Bio::Graphics::Glyph::pairplot(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::pairplot(3pm)
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);
}
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
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::Graphics::Glyph::xyplot, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
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 v5.14.2 2012-02-20 Bio::Graphics::Glyph::pairplot(3pm)