Bio::Graphics::Glyph::graded_segments(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::graded_segments(3pm)
NAME
Bio::Graphics::Glyph::graded_segments - The "graded_segments" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This is identical to the "alignment" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity
of each segment is proportionate to the score.
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
-connector Connector type 0 (false)
-connector_color
Connector color black
-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 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" attribute
-vary_fg Vary the foreground color as 0 (false)
well as the background
-merge_parts 0 (false)
Whether to simplify the
alignment at low magnification
-max_gap Do not merge across gaps Calculated
that exceed this threshold
If max_score and min_score are not specified, then the glyph will calculate the local maximum and minimum scores at run time. Since many
scoring functions are exponential you may wish to take the log of your scores before passing them to this glyph.
Simplifying the display of alignment features for large segments
The "merge_parts" option is used for semantic zooming. Specifically, if features are small and dense, they will not be displayed very well
for large segments and the color-coding will be lost. If merge-parts is set to a true value, adjacent alignment parts will be merged until
a gap exceeding a calculated or user-specified value is encountered. Unless specified, the maximum gap allowed for merging adjacent
features is calculated as (L/10000)*(L/500), where L = the length of the sequence displayed in the browser. The exponentially increasing
gap threshold allows more aggressive merging of alignment features as the size of the displayed sequence grows larger.
The score of the merged feature is calculated as a weighted average. For example, consider two adjacent HSPs that are each 400 bp in
length and have scores of 60% and 70%. If the merge_parts option is set to a true value, the two HSPs would be merged in the display to a
single 800 bp alignment block with an average score of 65%.
The merge_parts option is turned off by default.
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
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 v5.14.2 2012-02-20 Bio::Graphics::Glyph::graded_segments(3pm)