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.AUTHOR
Lincoln Stein <[email protected]>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.