Bio::G...y_plot(3pm)

✨ NAME ✨

Bio::Graphics::Glyph::ternary_plot — the glyph that draws ternary plot data 💅

(also this page is Bio::G...y_plot(3pm) from the User Contributed Perl Documentation, since the title got cutely truncated by the man renderer, love that for it 🎀)

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🌈 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;

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🦋 DESCRIPTION 🦋

okay so bestie, picture this: this glyph draws a light gray equilateral triangle, and its base is centered on the feature. 🫶 The top of that equilateral triangle is equal to the height you specify. And like, if you want it to look good — and we do want it to look good — please choose a height of >= 15. no cap. 💖

Inside, the glyph will plot one or more data points using ternary plot conventions (see http://en.wikipedia.org/wiki/Ternary_plot). The data is 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. So the way that this works: as a component approaches 1.0, it gets closer to its corresponding vertex. iconic behavior honestly 👑

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. 🎨 (yes it just vibes with the background, we love a low-effort queen)

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💜 OPTIONS 💜

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

• -triples — The callback to return triple data. 📞✨
• -vertices — Labels for the left,right & top vertices. 🏷️

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💀 BUGS 💀

Please report them. (yes that's the whole thing, they really said "your problem now" 😭 but fr fr, report them 🫶)

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👑 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

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🌸 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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and that's the whole page bestie!! this one was shipped as part of perl v5.30.0, dated 2019-11-25, in the User Contributed Perl Documentation section — so like, it's been serving looks since 2006 and still ate. periodt. 💖✨