Bio::Graphics::Glyph::UsereContributed Perl DoBio::Graphics::Glyph::protein(3)NAMEBio::Graphics::Glyph::protein - The "protein" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph draws protein sequences. At high magnifications, this glyph
will draw the actual amino acids of the sequence. At low
magnifications, the glyph will plot the Kyte-Doolite hydropathy. By
default, the KD plot will use a window size of 9 residues, but this can
be changed by specifying the kd_window option.
The feature may return either a protein sequence or a DNA sequence in
response to the seq() method. However, if it returns a DNA sequence,
then the feature must also return the correct phase and strand in order
for the glyph to translate its open reading frame correctly!
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_kd Whether to draw the Kyte- true
Doolittle hydropathy plot
at low mags
-kd_window Size of the sliding window 9
to use in the KD hydropathy
calculation.
-axis_color Color of the vertical axes fgcolor
in the KD hydropathy plot
-phase_style The way phase is to be
interpreted. One of "012"
"012" or "021"
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
Aaron J. Mackey, based on the "dna" glyphy by Lincoln Stein
<lstein@cshl.org> and Peter Ashton <pda@sanger.ac.uk>.
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 v5.14.1 2011-07-22 Bio::Graphics::Glyph::protein(3)
