Bio::Graphics::Glyph::stackedplot(3pm)			User Contributed Perl Documentation		    Bio::Graphics::Glyph::stackedplot(3pm)

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 v5.14.2							    2012-02-20				    Bio::Graphics::Glyph::stackedplot(3pm)