Bio::Graphics::Glyph::phylo_align(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::phylo_align(3pm)
NAME
Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph draws a cladogram for any set of species along with their alignment data in relation to the reference species. At high
magnification, base pair alignements will be displayed. At lower magnification, a conservation score plot will be drawn. Gaps as
specified by CIGAR are supported. Currently the scores are drawn to a log plot with the restriction that the score will be the same across
all base pairs within an alignment. It is hoped that this restriction can be addressed in the future.
For this glyph to work, the feature must return a DNA sequence string in response to the dna() method. Also, a valid tree file must be
available in a format readable by the Bio::Tree library.
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
------ ----------- -------
-draw_clado_left
Draws the Cladogram on left 0
-species_spacing
Spacing of species in DNA 1
mode in units of font height
-species_spacing_score
Spacing of spcies in 5
conservation view in units
of font height
-hide_label Whether to label spcies 0
-tree_file Path of file containing undef
cladogram tree information
-tree_format Format of tree file newick
-axis_color Color of the vertical axes fgcolor
in the GC content graph
-errcolor Color of all misalignment fgcolor
indicators
-mid_axis_color
Color of the middle axis of
the conservation score graph axis_color
-clado_bg Color of the clado bg bgcolor
indicators
-ref_color Color of base pair bg for bgcolor
the reference sequence
-targ_color Color of base pair bg for bgcolor
all base pairs that match
reference
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
AUTHORS
Hisanaga Mark Okada 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::phylo_align(3pm)