SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph is used for drawing features associated with numeric data using ``box and whisker'' style data points, which display the mean value, extreme ranges and first and third quartiles (or standard deviation). The boxes drawn by this glyph are similar to <http://www.abs.gov.au/websitedbs/D3310116.NSF/0/3c35ac1e828c23ef4a2567ac0020ec8a?OpenDocument>, except that they are oriented vertically so that the position and height of the box indicates the mean value and spread of the data, and the width indicates the genomic extent of the value.Like the xyplot glyph (from which it inherits the whiskerplot is designed to work on a single feature group that contains subfeatures. It is the subfeatures that carry the score information. The best way to arrange for this is to create an aggregator for the feature. We'll take as an example a histogram of repeat density in which interval are spaced every megabase and the score indicates the number of repeats in the interval; we'll assume that the database has been loaded in in such a way that each interval is a distinct feature with the method name ``density'' and the source name ``repeat''. Furthermore, all the repeat features are grouped together into a single group (the name of the group is irrelevant). If you are using Bio::DB::GFF and Bio::Graphics directly, the sequence of events would look like this:
my $agg = Bio::DB::GFF::Aggregator->new(-method => 'repeat_density',
-sub_parts => 'density:repeat');
my $db = Bio::DB::GFF->new(-dsn=>'my_database',
-aggregators => $agg);
my $segment = $db->segment('Chr1');
my @features = $segment->features('repeat_density');
my $panel = Bio::Graphics::Panel->new;
$panel->add_track(\@features,
-glyph => 'xyplot',
-scale => 'both',
);
If you are using Generic Genome Browser, you will add this to the configuration file:
aggregators = repeat_density{density:repeat}
clone alignment etc
Note that it is a good idea to add some padding to the left and right of the panel; otherwise the scale will be partially cut off by the edge of the image.
The mean (or median) of the data will be taken from the feature score. The range and quartile data must either be provided in a feature tag named ``range'', or must be generated dynamically by a -range callback option passed to add_track. The data returned by the tag or option should be an array reference containing the following five fields:
[$median,$range_low,$range_high,$quartile_low,$quartile_high]
where $range_low and $range_high correspond to the low and high value of the ``whiskers'' and $quartile_low and $quartile_high correspond to the low and high value of the ``box.''
If $median is undef or missing, then the score field of the feature will be used instead. It may be useful to repeat the median in the score field in any case, in order to allow the minimum and maximum range calculations of the graph itself to occur.
See Examples for three ways of generating an image.
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
------ ----------- -------
-range Callback to return median, none - data comes from feature "range" tag
range and quartiles for each
sub feature
EXAMPLES
Here are three examples of how to use this glyph.Example 1: Incorporating the numeric data in each subfeature
#!/usr/bin/perl
use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $bsg = 'Bio::SeqFeature::Generic';
my $feature = $bsg->new(-start=>0,-end=>1000);
for (my $i=0;$i<1000;$i+=20) {
my $y = (($i-500)/10)**2;
my $range = make_range($y);
my $part = $bsg->new(-start=>$i,-end=>$i+16,
-score=>$y,-tag => { range=>$range });
$feature->add_SeqFeature($part);
}
my $panel = Bio::Graphics::Panel->new(-length=>1000,-width=>800,-key_style=>'between',
-pad_left=>40,-pad_right=>40);
$panel->add_track($feature,
-glyph=>'arrow',
-double=>1,
-tick=>2);
$panel->add_track($feature,
-glyph=>'whiskerplot',
-scale=>'both',
-height=>200,
-min_score => -500,
-key =>'Whiskers',
-bgcolor => 'orange',
);
print $panel->png;
sub make_range {
my $score = shift;
my $range_top = $score + 5*sqrt($score) + rand(50);
my $range_bottom = $score - 5*sqrt($score) - rand(50);
my $quartile_top = $score + 2*sqrt($score) + rand(50);
my $quartile_bottom = $score - 2*sqrt($score) - rand(50);
return [$score,$range_bottom,$range_top,$quartile_bottom,$quartile_top];
}
Example 2: Generating the range data with a callback
#!/usr/bin/perl
use strict;
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $bsg = 'Bio::SeqFeature::Generic';
my $feature = $bsg->new(-start=>0,-end=>1000);
for (my $i=0;$i<1000;$i+=20) {
my $y = (($i-500)/10)**2;
my $part = $bsg->new(-start=>$i,-end=>$i+16,-score=>$y);
$feature->add_SeqFeature($part);
}
my $panel = Bio::Graphics::Panel->new(-length=>1000,-width=>800,-key_style=>'between',
-pad_left=>40,-pad_right=>40);
$panel->add_track($feature,
-glyph=>'arrow',
-double=>1,
-tick=>2);
$panel->add_track($feature,
-glyph=>'whiskerplot',
-scale=>'both',
-height=>200,
-min_score => -500,
-key =>'Whiskers',
-bgcolor => 'orange',
-range => \&make_range,
);
print $panel->png;
sub make_range {
my $feature = shift;
my $score = $feature->score;
my $range_top = $score + 5*sqrt($score) + rand(50);
my $range_bottom = $score - 5*sqrt($score) - rand(50);
my $quartile_top = $score + 2*sqrt($score) + rand(50);
my $quartile_bottom = $score - 2*sqrt($score) - rand(50);
return [$score,$range_bottom,$range_top,$quartile_bottom,$quartile_top];
}
Example 3: Generating the image from a FeatureFile
- The file:
-
[general] pixels = 840 pad_left = 40 pad_right = 40 [contig] glyph = arrow double = 1 tick = 2 [data] glyph = whiskerplot scale = both height = 200 min_score = -500 max_score = 2800 key = Whiskers bgcolor = orange chr1 . contig 1 1000 . . . Contig chr1 chr1 . data 0 16 2500 . . Dataset data1; range 2209,2769,2368,2619 chr1 . data 20 36 2304 . . Dataset data1; range 2051,2553,2163,2435 chr1 . data 40 56 2116 . . Dataset data1; range 1861,2384,1983,2253 chr1 . data 60 76 1936 . . Dataset data1; range 1706,2181,1819,2059 chr1 . data 80 96 1764 . . Dataset data1; range 1516,1995,1646,1849 chr1 . data 100 116 1600 . . Dataset data1; range 1359,1834,1513,1699 chr1 . data 120 136 1444 . . Dataset data1; range 1228,1654,1330,1565 chr1 . data 140 156 1296 . . Dataset data1; range 1105,1520,1198,1385 chr1 . data 160 176 1156 . . Dataset data1; range 983,1373,1062,1270 chr1 . data 180 196 1024 . . Dataset data1; range 853,1184,914,1116 chr1 . data 200 216 900 . . Dataset data1; range 722,1093,801,965 chr1 . data 220 236 784 . . Dataset data1; range 621,945,724,859 chr1 . data 240 256 676 . . Dataset data1; range 532,833,605,742 chr1 . data 260 276 576 . . Dataset data1; range 433,714,485,653 chr1 . data 280 296 484 . . Dataset data1; range 331,600,418,545 chr1 . data 300 316 400 . . Dataset data1; range 275,535,336,459 chr1 . data 320 336 324 . . Dataset data1; range 198,434,270,374 chr1 . data 340 356 256 . . Dataset data1; range 167,378,219,322 chr1 . data 360 376 196 . . Dataset data1; range 114,303,118,249 chr1 . data 380 396 144 . . Dataset data1; range 39,248,87,197 chr1 . data 400 416 100 . . Dataset data1; range 17,173,68,141 chr1 . data 420 436 64 . . Dataset data1; range -14,125,18,84 chr1 . data 440 456 36 . . Dataset data1; range -8,74,11,64 chr1 . data 460 476 16 . . Dataset data1; range -46,77,0,43 chr1 . data 480 496 4 . . Dataset data1; range -40,43,-7,36 chr1 . data 500 516 0 . . Dataset data1; range -43,0,-43,22 chr1 . data 520 536 4 . . Dataset data1; range -6,52,-4,54 chr1 . data 540 556 16 . . Dataset data1; range -5,38,-27,52 chr1 . data 560 576 36 . . Dataset data1; range -43,109,18,66 chr1 . data 580 596 64 . . Dataset data1; range -1,134,3,112 chr1 . data 600 616 100 . . Dataset data1; range 49,186,69,124 chr1 . data 620 636 144 . . Dataset data1; range 79,225,71,169 chr1 . data 640 656 196 . . Dataset data1; range 124,289,120,266 chr1 . data 660 676 256 . . Dataset data1; range 154,378,197,320 chr1 . data 680 696 324 . . Dataset data1; range 220,439,249,396 chr1 . data 700 716 400 . . Dataset data1; range 291,511,331,458 chr1 . data 720 736 484 . . Dataset data1; range 350,627,400,572 chr1 . data 740 756 576 . . Dataset data1; range 446,718,502,633 chr1 . data 760 776 676 . . Dataset data1; range 515,833,576,777 chr1 . data 780 796 784 . . Dataset data1; range 606,959,724,856 chr1 . data 800 816 900 . . Dataset data1; range 747,1058,799,1004 chr1 . data 820 836 1024 . . Dataset data1; range 817,1231,958,1089 chr1 . data 840 856 1156 . . Dataset data1; range 961,1341,1069,1225 chr1 . data 860 876 1296 . . Dataset data1; range 1103,1511,1219,1385 chr1 . data 880 896 1444 . . Dataset data1; range 1218,1660,1338,1535 chr1 . data 900 916 1600 . . Dataset data1; range 1377,1828,1496,1703 chr1 . data 920 936 1764 . . Dataset data1; range 1547,2020,1674,1858 chr1 . data 940 956 1936 . . Dataset data1; range 1691,2188,1824,2043 chr1 . data 960 976 2116 . . Dataset data1; range 1869,2376,2019,2225 chr1 . data 980 996 2304 . . Dataset data1; range 2040,2554,2178,2418
- The script to render it
-
#!/usr/bin/perl use strict; use Bio::Graphics::FeatureFile; my $data = Bio::Graphics::FeatureFile->new(-file=>'test.gff'); my(undef,$panel) = $data->render; print $panel->png;
BUGS
Please report them.AUTHOR
Lincoln Stein <[email protected]>Copyright (c) 2001 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.