Bio::Graphics::Glyph::dna - The "dna" glyph

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS

- BUGS
- SEE ALSO
- AUTHOR

# NAME

Bio::Graphics::Glyph::dna - The "dna" glyph

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# SYNOPSIS

      See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

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# 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 the Bio::Graphics::Glyph manpage 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.

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# BUGS

Please report them.

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# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::triangle manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, GD

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# 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.

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Bio::Graphics::Glyph::dna - The "dna" glyph