Bio::Graphics::Glyph::UseroContributed Perl DocBio::Graphics::Glyph::xyplot(3)NAMEBio::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.
perl v5.14.1 2011-07-22 Bio::Graphics::Glyph::xyplot(3)
