Lincoln D. Stein > Bio-Graphics-2.37 > Bio::Graphics::Glyph::ternary_plot

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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.

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