NAME
Bio::Graphics::Glyph::dna - The "dna" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.DESCRIPTION
This glyph draws DNA sequences. At high magnifications, this glyph will draw the actual base pairs of the sequence (both strands). At low magnifications, the glyph will plot the GC content. By default, the GC calculation will use non-overlapping bins, but this can be changed by specifying the gc_window option, in which case, a sliding window calculation will be used.
For this glyph to work, the feature must return a Bio::PrimarySeq DNA object in response to the seq() method. For example, you can use a Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq like this:
my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end => 800 );
$feature->attach_seq($dna);
$panel->add_track( $feature, -glyph => 'dna' );A Bio::Graphics::Feature object may also be used.
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 to the common options, the following glyph-specific options are recognized:
Option Description Default
------ ----------- -------
-do_gc Whether to draw the GC true
graph at low mags
-gc_window Size of the sliding window E<lt>noneE<gt>
to use in the GC content
calculation. If this is
not defined, non-
overlapping bins will be
used. If this is set to
"auto", then the glyph will
choose a window equal to
1% of the interval.
-gc_bins Fixed number of intervals 100
to sample across the
panel.
-axis_color Color of the vertical axes fgcolor
in the GC content graph
-strand Show both forward and auto
reverse strand, one of
"forward", "reverse",
"both" or "auto".
In "auto" mode,
+1 strand features will
show the plus strand
-1 strand features will
show the reverse complement
and strandless features will
show bothNOTE: -gc_window=>'auto' gives nice results and is recommended for drawing GC content. The GC content axes draw slightly outside the panel, so you may wish to add some extra padding on the right and left.
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>.
Sliding window GC calculation added by Peter Ashton <pda@sanger.ac.uk>.
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.