See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTIONThis 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.
OPTIONSThe 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 both
NOTE: -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.
BUGSPlease report them.
AUTHORLincoln Stein <[email protected]>.
Sliding window GC calculation added by Peter Ashton <[email protected]>.
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.