Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
Bio::Graphics::Glyph::UserpContributed Perl DBio::Graphics::Glyph::pairplot(3)

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

	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 = $start+120;
					   -end	 =>$end
	  $start += 200;

			  -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);

       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

       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.

       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

       Please report them.

       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::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

       Lincoln Stein <<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 v5.32.1			  2021-11-06 Bio::Graphics::Glyph::pairplot(3)


Want to link to this manual page? Use this URL:

home | help