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Bio::Graphics::Glyph::UserkContributed PerBio::Graphics::Glyph::stackedplot(3)

NAME
       Bio::Graphics::Glyph::stackedplot - The stackedplot glyph

SYNOPSIS
	 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION
       The stackedplot glyph can be used to draw quantitative feature data
       using a stacked column plot. It differs from the	xyplot glyph in	that
       the plot	applies	to a single top	level feature, not a group of
       subfeatures. The	data to	be graphed is derived from an attribute	called
       "data_series."

       The data	to be graphed is represented as	a list of arrays:

	(
	[1, 2, 8],
	[6, 1, 1],
	[10,8, 0],
	[1, 1, 1],
	)

       Each array is a column in the stacked plot. Its values become the
       subdivisions of the column. In this example, there are four columns,
       each of which has three subdivisions.

       You can add labels to the columns and change the	colors of the
       subdivisions.

       To assign data to a feature, you	can add	a "series" tag:

	$snp1	 = Bio::SeqFeature::Generic ->new (-start     => 500,-end=>501,
						   -display_name =>'example',
						   -tag=> { series => [
								    [10,20,30],
								    [30,30,0],
								    [5,45,10],
								    [5,45,10],
								    [5,45,10],
								    [50,0,50],
								   ],
							    }
						      );

       Note that the series tag	must consist of	an array of arrays.

       If you are using	a gff3 representation, you can load a database with
       data that looks like this:

	chr1 test feature 1 1000 . . . series=10 20 30;series=30 30 0;series=5 45 10...

       If you are using	a gff2 representation, you can load a database with
       data that looks like this:

	chr1 test feature 1 1000 . . . series 10 20 30;	series 30 30 0 series 5	45 10...

       Or you can pass a callback to the -series option:

	$panel->add_track(\@data,
			 -glyph	    => 'stackedplot',
			 -series       => sub {
					 my $feature = shift;
				    return [
				       [10,20,30],
				       [30,30,0],
				       [5,45,10],
				   ]
				 }
			);

   OPTIONS
       The following options are standard among	all Glyphs.  See
       Bio::Graphics::Glyph for	a full explanation.

	 Option	     Description		      Default
	 ------	     -----------		      -------

	 -fgcolor      Foreground color		      black

	 -outlinecolor Synonym for -fgcolor

	 -bgcolor      Background color		      turquoise

	 -fillcolor    Synonym for -bgcolor

	 -linewidth    Line width		      1

	 -height       Height of glyph		      10

	 -font	       Glyph font		      gdSmallFont

	 -label	       Whether to draw a label	      0	(false)

	 -description  Whether to draw a description  0	(false)

	 -hilite       Highlight color		      undef (no	color)

       In addition, the	alignment glyph	recognizes all the options of the
       xyplot glyph, as	well as	the following glyph-specific option:

	 Option		Description		     Default
	 ------		-----------		     -------

	-fixed_gap     Vertical	distance between      8
		       the rectangle that shows
		       the start:end range of
		       the feature and the fixed
		       width stacked plot.

	-series_colors A list giving a series of     red,blue,green,orange,
		       color names for the data	     brown,grey,black
		       series (the values inside
		       each stacked column).

	-column_labels A list of labels	to print     -none-
		       underneath each column.

	-column_width  The width of each column.     8

	-column_spacing	Spacing	between	each	     2
		       column.

	-min_score     Minimum score for the	     0.0
		       sum of the members of
		       each data series.

	-max_score     Maximum score for the	     1.0
		       sum of the members of each
		       data series.

	-scale_font    Font to use for the scale.    gdTinyFont

	-column_font   Font to use for the column    gdSmallFont
		       labels.

	-draw_scale    Whether to draw a scale to    true
		       right of	the columns.

       Note that -min_score and	-max_score represent the minimum and maximum
       SUM of all the values in	the data series. For example, if your largest
       column contains the series (10,20,30), then the -max_score is 60.

EXAMPLE
       To understand how this glyph works, try running and modifying the
       following example:

	#!/usr/bin/perl

	use strict;
	use warnings;

	use Bio::Graphics;
	use Bio::SeqFeature::Generic;

	my $segment  = Bio::Graphics::Feature->new(-start=>1,-end=>700);

	my $snp1     = Bio::SeqFeature::Generic	->new (-start	  => 500,-end=>590,
						       -display_name =>'fred',
						       -tag=> {	series => [
									    [10,20,30],
									    [30,30,0],
									    [5,45,10],
									    [5,45,10],
									    [5,45,10],
									    [50,0,50],
									   ],
							     },
						       -source=>'A test',
						       );

	my $snp2     = Bio::SeqFeature::Generic->new(-start	=> 300,
						     -end	=> 301,
						     -display_name  => 'rs12345',
						     -tag=> {
							    series => [
									    [30,20,10 ],
									    [80,10,10 ],
								      ],
							   },
						     -source=>'Another test',
						   );

	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],
			  -height    =>	50,
			  -glyph     =>	'stackedplot',
			  -fixed_gap =>	12,
			  -series_colors    => [qw(red blue lavender)],
			  -column_labels => [qw(a b c d	e f g)],
			  -min_score =>	0,
			  -max_score =>	100,
			  -column_width	=> 8,
			  -column_font	=> 'gdMediumBoldFont',
			  -scale_font	=> 'gdTinyFont',
			  -label    => 1,
			  -description=>1,
			 );
	print $panel->png;

BUGS
       Please report them.

SEE ALSO
       Bio::Graphics::Panel, Bio::Graphics::Track,
       Bio::Graphics::Glyph::transcript2,
       Bio::Graphics::Glyph::anchored_arrow, Bio::Graphics::Glyph::arrow,
       Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::primers,
       Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::toomany,
       Bio::Graphics::Glyph::transcript,

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 v5.32.1			  2021-11-Bio::Graphics::Glyph::stackedplot(3)

NAME | SYNOPSIS | DESCRIPTION | EXAMPLE | BUGS | SEE ALSO | AUTHOR

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