| Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph |
Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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.
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 ------ ----------- -------
-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
Please report them.
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
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.
| Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph |