Bio::Graphics::Glyph::UserlContributed PeBio::Graphics::Glyph::allele_tower(3)NAMEBio::Graphics::Glyph::allele_tower - The "allele_tower" glyph
SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
DESCRIPTION
This glyph draws a letter for each allele found at a SNP position, one
above the other (i.e. in a column). For example:
A
G
See also http://www.hapmap.org/cgi-perl/gbrowse/gbrowse 'genotyped
SNPs' for an example.
The common options are available (except height which is calculated
based on the number of alleles). In addition, if you give the glyph
the minor allele frequency (MAF) and indicate which is the minor
allele, the glyph will display these differences.
GETTING THE ALLELES
To specify the alleles, create an "Alleles" attribute for the feature.
There should be two such attributes. For example, for a T/G
polymorphism, the GFF load file should look like:
Chr3 . SNP 12345 12345 . . . SNP ABC123; Alleles T ; Alleles G
Alternatively, you can pass an "alleles" callback to the appropriate
section of the config file. This option should return the two alleles
separated by a slash:
alleles = sub {
my $snp = shift;
my @d = $snp->attributes('AllelePair');
return join "/",@d;
}
OPTIONS
. Glyph Colour
. Different colour for alleles on the reverse strand
. Print out the complement for alleles on the reverse strand
. Major allele shown in bold
. Horizontal histogram to show allele frequency
GLYPH COLOR
The glyph color can be configured to be different if the feature is on
the plus or minus strand. Use fgcolor to define the glyph color for
the plus strand and bgcolor for the minus strand. For example:
fgcolor = blue
bgcolor = red
For this option to work, you must also set ref_strand to return the
strand of the feature:
ref_strand = sub {shift->strand}
REVERSE STRAND ALLELES
If the alleles on the negative strand need to be the complement of what
is listed in the GFF files, (e.g. A/G becomes T/C), set the complement
option to have value 1
complement = 1
For this option to work, you must also set ref_strand to return the
strand of the feature:
ref_strand = sub {shift->strand}
MAJOR/MINOR ALLELE
Use the 'minor_allele' option to return the minor allele for the SNP.
If you use this option, the major allele will appear in bold type.
ALLELE FREQUENCY HISTOGRAMS
Use the 'maf' option to return the minor allele frequency for the SNP.
If you use this option, a horizontal histogram will be drawn next to
the alleles, to indicate their relative frequencies. e.g.
A______
C__
Note: The 'label' option must be set to 1 (i.e. on) and the
'minor_allele' option must return a valid allele for this to work.
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::allele_tower, Bio::DB::GFF, Bio::SeqI,
Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Fiona Cunningham <cunningh@cshl.edu> in Lincoln Stein's lab
<steinl@cshl.edu>.
Copyright (c) 2003 Cold Spring Harbor Laboratory
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the GPL (either
version 1, or at your option, any later version) or the Artistic
License 2.0. Refer to LICENSE for the full license text. In addition,
please see DISCLAIMER.txt for disclaimers of warranty.
perl v5.14.12011-07Bio::Graphics::Glyph::allele_tower(3)
