Bio::Graphics::Glyph::gene(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::gene(3pm)
NAME
Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other
and given a single label and description that apply to the entire stack. Each individual transcript's name is optionally printed to the
left of the transcript glyph.
Transcripts (splice isoforms) are drawn using the processed_transcript glyph. CDS features are drawn in the background color, and the UTRs
are drawn in an alternate color selected by the utr_color option. In addition, you can make the UTRs thinner than the CDS by setting the
"thin_utr" option.
This glyph is designed to work properly with GFF3-style three-tier genes, in which the top level feature has the Sequence Ontology type of
"gene", the second level feature(s) have the SO type "mRNA", and the third level feature(s) have the SO type "CDS", "five_prime_utr" and
"three_prime_utr." Subparts named "UTR" are also honored. The feature can contain other subparts as well (e.g. exon, intron,
translation), but they are currently ignored unless the option sub_part is supplied. If the sub_part option is used that feature type will
be used and CDS and UTR features will be excluded. This could be used for specifying that exons be used instead, for example.
This glyph is a subclass of processed_transcript, and recognizes the same options.
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 undef (false)
-connector_color
Connector color black
-label Whether to draw a label undef (false)
-description Whether to draw a description undef (false)
-strand_arrow Whether to indicate undef (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the gene glyph recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------
-label_transcripts undef (false)
Flag. If true, then the
display name of each
transcript will be drawn
to the left of the transcript
glyph.
-thin_utr Flag. If true, UTRs will undef (false)
be drawn at 2/3 of the
height of CDS segments.
-utr_color Color of UTR segments. Gray #D0D0D0
-decorate_introns
Draw strand with little arrows undef (false)
on the intron.
The -adjust_exons and -implied_utrs options are inherited from processed_transcript, but are quietly ignored. Please use the
processed_transcript glyph for this type of processing.
BUGS
The SO terms are hard-coded. They should be more flexible and should recognize ISA relationships.
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::gene(3pm)