Bio::Graphics::Glyph::ternary_plot(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::ternary_plot(3pm)
NAME
Bio::Graphics::Glyph::ternary_plot - Draw ternary plot data
SYNOPSIS
#!/usr/bin/perl
use strict;
use warnings;
use Bio::Graphics;
use Bio::Graphics::Feature;
my $segment = Bio::Graphics::Feature->new(-start=>1,-end=>700);
my $snp1 = Bio::Graphics::Feature->new(-start => 500,
-end => 501,
-name => 'rs000001',
-attributes=> {triples => [
[0.01, 0.81, 0.18, 'red', 'CEPH'],
[0.25, 0.25, 0.50, 'blue', 'JPT+CHB'],
[0.81, 0.01, 0.18, 'green','YRI'],
]
}
);
my $snp2 = Bio::Graphics::Feature->new(-start => 300,
-end => 301,
-name => 'rs12345',
-attributes=> {triples => [
[0.04, 0.64, 0.32, 'red', 'Controls'],
[0.16, 0.36, 0.48, 'blue', 'Cases'],
]
}
);
my $panel = Bio::Graphics::Panel->new(-segment=>$segment,-width=>800);
$panel->add_track($segment,-glyph=>'arrow',-double=>1,-tick=>2);
$panel->add_track([$snp1,$snp2],
-glyph => 'ternary_plot',
-height => 80,
-fgcolor => 'lightgrey',
-vertices => ['AA','GG','AG'],
-label => 1,
);
print $panel->png;
DESCRIPTION
This glyph draws a light gray equilateral triangle with its base centered on the feature. The top of the equilateral triangle is equal to
the specified height. To look good, please choose a height of >= 15.
Inside, the glyph will plot one or more data points using ternary plot conventions (see http://en.wikipedia.org/wiki/Ternary_plot). The
data consists of a series of (A,B,C) triplets chosen such that the range of each component is [0.0,1.0] and A + B + C = 1.0. The left,
right and apex of the triangle represent the proportions of A, B and C respectively. As a component approaches 1.0, it gets closer to its
corresponding vertex.
The data can be represented as one or more feature tags called "triples" each in the format:
A1,B1,C1,<color>,<label> # (color and label are optional)
or as a callback specified by the option -triples, which should return a list of arrays, where each array is a triple, followed by an
optional color. E.G.
sub my_calback {
my $feature = shift;
return [[0.1,0.5,0.4,'red','pt1'],[0.2,0.2,0.6,'blue','pt2'],[0.8,0.2,0.0,'green','pt4']];
}
The color, if it is missing, will be the same as the bgcolor.
OPTIONS
In addition to the common options, the following glyph-specific options are recognized:
Option Description
------ -----------
-triples The callback to return triple data.
-vertices Labels for the left,right & top vertices
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::whiskerplot, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2006 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.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::ternary_plot(3pm)