Provided by: libbio-graphics-perl_2.40-2_all 
NAME
Bio::Graphics::Glyph::xyplot - The xyplot glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph is used for drawing features that have a position on the genome and a numeric
value. It can be used to represent gene prediction scores, motif-calling scores, percent
similarity, microarray intensities, or other features that require a line plot.
The X axis represents the position on the genome, as per all other glyphs. The Y axis
represents the score. Options allow you to set the height of the glyph, the maximum and
minimum scores, the color of the line and axis, and the symbol to draw.
The plot 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(-pad_left=>40,-pad_right=>40);
$panel->add_track(\@features,
-glyph => 'xyplot',
-graph_type=>'points',
-point_symbol=>'disc',
-point_radius=>4,
-scale=>'both',
-height=>200,
);
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 "boxes" variant allows you to specify a pivot point such that scores above the pivot
point are drawn in one color, and scores below are drawn in a different color. These
"bicolor" plots are controlled by the options -bicolor_pivot, -pos_color and -neg_color,
as described below.
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 xyplot glyph recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------
-max_score Maximum value of the Calculated
feature's "score" attribute
-min_score Minimum value of the Calculated
feature's "score" attributes
-graph_type Type of graph to generate. Histogram
Options are: "histogram",
"boxes", "line", "points",
or "linepoints".
-point_symbol Symbol to use. Options are none
"triangle", "square", "disc",
"filled_triangle",
"filled_square",
"filled_disc","point",
and "none".
-point_radius Radius of the symbol, in 4
pixels (does not apply
to "point")
-scale Position where the Y axis none
scale is drawn if any.
It should be one of
"left", "right", "both" or "none"
-graph_height Specify height of the graph Same as the
"height" option.
-part_color For boxes & points only, none
bgcolor of each part (should
be a callback). Supersedes
-neg_color.
-scale_color Color of the scale Same as fgcolor
-clip If min_score and/or max_score false
are manually specified, then
setting this to true will
cause values outside the
range to be clipped.
-bicolor_pivot 0
Where to pivot the two colors
when drawing bicolor plots.
Scores greater than this value will
be drawn using -pos_color.
Scores lower than this value will
be drawn using -neg_color.
-pos_color When drawing bicolor plots, same as bgcolor
the fill color to use for
values that are above
the pivot point.
-neg_color When drawing bicolor plots, same as bgcolor
the fill color to use for values
that are below the pivot point.
Note that when drawing scales on the left or right that the scale is actually drawn a few
pixels outside the boundaries of the glyph. You may wish to add some padding to the image
using -pad_left and -pad_right when you create the panel.
The -part_color option can be used to color each part of the graph. Only the "boxes",
"points" and "linepoints" styles are affected by this. Here's a simple example:
$panel->add_track->(\@affymetrix_data,
-glyph => 'xyplot',
-graph_type => 'boxes',
-part_color => sub {
my $score = shift->score;
return 'red' if $score < 0;
return 'lightblue' if $score < 500;
return 'blue' if $score >= 500;
}
);
METHODS
For those developers wishing to derive new modules based on this glyph, the main method to
override is:
'method_name' = $glyph->lookup_draw_method($type)
This method accepts the name of a graph type (such as 'histogram') and returns the
name of a method that will be called to draw the contents of the graph, for example
'_draw_histogram'. This method will be called with three arguments:
$self->$draw_method($gd,$left,$top,$y_origin)
where $gd is the GD object, $left and $top are the left and right positions of the
whole glyph (which includes the scale and label), and $y_origin is the position of the
zero value on the y axis (in pixels). By the time this method is called, the y axis
and labels will already have been drawn, and the scale of the drawing (in pixels per
unit score) will have been calculated and stored in $self->{_scale}. The y position
(in pixels) of each point to graph will have been stored into the part, as
$part->{_y_position}. Hence you could draw a simple scatter plot with this code:
sub lookup_draw_method {
my $self = shift;
my $type = shift;
if ($type eq 'simple_scatterplot') {
return 'draw_points';
} else {
return $self->SUPER::lookup_draw_method($type);
}
}
sub draw_points {
my $self = shift;
my ($gd,$left,$top) = @_;
my @parts = $self->parts;
my $bgcolor = $self->bgcolor;
for my $part (@parts) {
my ($x1,$y1,$x2,$y2) = $part->calculate_boundaries($left,$top);
my $x = ($x1+$x2)/2; # take center
my $y = $part->{_y_position};
$gd->setPixel($x,$y,$bgcolor);
}
lookup_draw_method() may return multiple method names if needed. Each will be called
in turn.
$y_position = $self->score2position($score)
Translate a score into a y pixel position, obeying clipping rules and min and max
values.
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) 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.