package Bio::Graphics::Glyph::stackedplot;
use strict;
use base 'Bio::Graphics::Glyph::fixedwidth';
use GD::Simple;
use Carp 'cluck';
use Memoize;
memoize('scale_width');
memoize('width_needed');
sub width_needed {
my $self = shift;
my $column_width = $self->column_width;
my $column_spacing = $self->column_spacing;
my $columns = $self->data_series;
my $needed = @$columns * ($column_width + $column_spacing);
return $needed;
}
#sub pad_right {
# my $self = shift;
# my $pr = $self->SUPER::pad_right;
# my $sw = $self->scale_width;
# return $pr+$sw;
#}
sub pad_right {
my $self = shift;
my $pr = $self->SUPER::pad_right;
my $sw = $self->scale_width + $self->column_width/2;
my $content_width = $self->width_needed;
my $total = $sw + $content_width;
my $additional = $pr - $total;
return $pr if $pr > $additional;
return $additional;
}
sub scale_width {
my $self = shift;
return 0 unless $self->do_draw_scale;
my ($min,$max) = $self->min_max;
my $middle = ($min+$max)/2;
my ($longest) = sort {$b<=>$a} map {length($_)} ($min,$middle,$max);
return $longest * $self->scale_font->width;
}
sub pad_bottom {
my $self = shift;
my @labels = $self->column_labels;
my $bottom = $self->SUPER::pad_bottom;
return $bottom unless @labels;
return $bottom + $self->font('gdTinyFont')->height;
}
sub column_width { shift->option('column_width') || 8 }
sub column_spacing { shift->option('column_spacing') || 2 }
sub maxdepth { 0 }
sub min_max {
my $self = shift;
my $min_score = $self->option('min_score') || 0.0;
my $max_score = $self->option('max_score') || 1.0;
return ($min_score,$max_score);
}
# this behaves more like the image glyph -- it draws a generic glyph, two diagonal lines, and then the
# plot underneath.
sub draw_contents {
my $self = shift;
my ($gd,$left,$top,$right,$bottom) = @_;
my ($min_score,$max_score) = $self->min_max;
my $height = $bottom-$top;
my $scale = $max_score > $min_score ? $height/($max_score-$min_score) : 1;
my $y_origin = $min_score <= 0 ? $bottom - (0 - $min_score) * $scale : $bottom;
my $scale_width = $self->scale_width;
$y_origin = $top if $max_score < 0;
$self->draw_stackedplot($gd,$left,$right,$top,$y_origin,$scale,$min_score,$max_score);
$self->draw_scale($gd,$left,$top,$right,$bottom);
}
sub draw_stackedplot {
my $self = shift;
my ($gd,$left,$right,$top,$bottom,$scale,$min,$max) = @_;
my $fgcolor = $self->fgcolor;
my $bgcolor = $self->bgcolor;
my @colors = $self->series_colors;
my @labels = $self->column_labels;
my $column_width = $self->column_width;
my $column_spacing = $self->column_spacing;
my $font = $self->column_font;
my $fwidth = $font->width;
my $fontcolor = $self->fontcolor;
# data_series() returns 1 or more values to stack upwards
# the totals of the values must be no greater than max_score
if (my $values = $self->data_series) {
my $x_offset = 0;
for (my $cluster = 0; $cluster < @$values; $cluster++) {
# this will give us a series of data series
my $series = $values->[$cluster];
my $y_offset = 0;
for (my $i = 0; $i < @$series; $i++) {
my $value = $series->[$i];
my $v = $self->clip($value,$min,$max);
my $color = $colors[$i] || $bgcolor;
my $y = $bottom - ($v-$min) * $scale;
my $box_bottom = $bottom - $y_offset;
my $box_top = $y - $y_offset;
$self->filled_box($gd,$left+$x_offset,$box_top,$left+$column_width+$x_offset,$box_bottom,$color);
$y_offset += $box_bottom-$box_top;
}
if (@labels) {
my $x = $left+$x_offset+($column_width-$fwidth*$labels[$cluster])/2-1;
$gd->string($font,$x,$bottom,$labels[$cluster],$fontcolor);
}
$x_offset += $column_spacing+$column_width;
}
}
}
sub clip {
my $self = shift;
my ($value,$min,$max) = @_;
$value = $min if defined $min && $value < $min;
$value = $max if defined $max && $value > $max;
return $value;
}
sub series_colors {
my $self = shift;
my $values = $self->option('series_colors');
my @colors;
if ($values && !ref $values) {
@colors = split /\s+/,$values;
} elsif (ref $values eq 'ARRAY') {
@colors = @$values;
} else {
@colors = qw(red blue green orange brown grey black);
}
return map {$self->translate_color($_)} @colors;
}
sub column_labels {
my $self = shift;
my $values = $self->option('column_labels');
my @labels;
if ($values && !ref $values) {
@labels = split /\s+/,$values;
} elsif (ref $values eq 'ARRAY') {
@labels = @$values;
}
return @labels;
}
# NOTE!
# probably data_series should return this:
# [series1 => [value1,value2,value3,value4],
# series2 => [value1,value2,value3,value4],
# series3 => [value1,value2,value3,value4],
# ...
# ]
sub data_series {
my $self = shift;
my $values = $self->option('series');
return $values if defined $values;
# otherwise get it from the feature
my @values;
my @tagvalues = $self->feature->get_tag_values('series');
for my $v (@tagvalues) {
if (ref $v && ref $v eq 'ARRAY') { # already in right format
push @values,$v;
} else {
push @values,[split /[,\s]+/,$v];
}
}
return \@values;
}
sub do_draw_scale {
my $self = shift;
my $drawit = $self->option('draw_scale');
return defined $drawit ? $drawit : 1;
}
sub scale_font {
my $self = shift;
$self->getfont('scale_font','gdTinyFont');
}
sub column_font {
my $self = shift;
$self->getfont('column_font','gdSmallFont');
}
sub draw_scale {
my $self = shift;
my ($gd,$left,$top,$right,$bottom) = @_;
my ($min,$max) = $self->min_max;
$self->panel->startGroup($gd);
my $simple = GD::Simple->new($gd);
$simple->font($self->scale_font);
my $dx = 1;
my $dy = $simple->font->height/2;
# these drew a vertical scale line, which didn't look very nice
# $simple->moveTo($right,$bottom);
# $simple->lineTo($right,$top);
$simple->moveTo($right,$top);
$simple->line(3);
$simple->move($dx,$dy);
$simple->string($max);
$simple->moveTo($right,($bottom+$top)/2);
$simple->line(3);
$simple->move($dx,$dy);
$simple->string(($max+$min)/2);
$simple->moveTo($right,$bottom);
$simple->line(3);
$simple->move($dx,$dy);
$simple->string($min);
$self->panel->endGroup($gd);
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::stackedplot - The stackedplot glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 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],
]
}
);
=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
------ ----------- -------
-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.
=head1 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;
=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) 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.
=cut