package Bio::Graphics::Glyph::whiskerplot;
use strict;
use base qw(Bio::Graphics::Glyph::xyplot);
sub lookup_draw_method {
my $self = shift;
return 'draw_whiskerplot';
}
sub draw_whiskerplot {
my $self = shift;
my ($gd,$left,$top) = @_;
my @parts = $self->parts;
my $fgcolor = $self->fgcolor;
for my $part (@parts) {
my ($x1,$y1,$x2,$y2) = $part->calculate_boundaries($left,$top);
my $y = $part->{_y_position};
# get the range and tendency
if (my $range = $part->get_range) {
unshift @$range,undef if @$range == 4; # backward compatibility
my ($median,$range_low,$range_high,$lower_quartile,$higher_quartile) = @$range;
$y = $part->{_y_position} = $self->score2position($median) if defined $median;
# draw the quartile box
my ($box_top,$box_bottom) = ($y,$y);
if (defined $lower_quartile && defined $higher_quartile) {
$box_top = $self->score2position($higher_quartile);
$box_bottom = $self->score2position($lower_quartile);
$self->filled_box($gd,$x1,$box_top,$x2,$box_bottom);
}
# calculate positions of the range whiskers
if (defined $range_low && defined $range_high) {
my $range_top = $self->score2position($range_high);
my $range_bottom = $self->score2position($range_low);
my $center = ($x1+$x2)/2;
my $whisker_left = $center-5;
my $whisker_right = $center+5;
$whisker_left = $x1 if $whisker_left < $x1;
$whisker_right = $x2 if $whisker_right > $x2;
# top whisker
$gd->line($center,$box_top,$center,$range_top,$fgcolor);
$gd->line($whisker_left,$range_top,$whisker_right,$range_top,$fgcolor);
# bottom whisker
$gd->line($center,$box_bottom,$center,$range_bottom,$fgcolor);
$gd->line($whisker_left,$range_bottom,$whisker_right,$range_bottom,$fgcolor);
}
}
# draw the median
$gd->line($x1,$y,$x2,$y,$fgcolor);
}
}
sub get_range {
my $self = shift;
my $range = $self->option('range');
return $range if defined $range;
# otherwise get it from the feature
return [$self->feature->get_tag_values('range')];
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::whiskerplot - The whiskerplot glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 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
L<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.
=head2 OPTIONS
The following options are standard among all Glyphs. See
L<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
=head1 EXAMPLES
Here are three examples of how to use this glyph.
=head2 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];
}
=head2 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];
}
=head2 Example 3: Generating the image from a FeatureFile
=over 4
=item 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
=item 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;
=back
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Track>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::anchored_arrow>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::box>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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.
=cut