Bio::Graphics::Glyph::allele_tower(3pm) 		User Contributed Perl Documentation		   Bio::Graphics::Glyph::allele_tower(3pm)

NAME

       Bio::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->get_tag_values('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 v5.14.2							    2012-02-20				   Bio::Graphics::Glyph::allele_tower(3pm)