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Bio::Graphics::Glyph::UserlContributed PeBio::Graphics::Glyph::allele_tower(3)

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 v5.24.1			  2017-07Bio::Graphics::Glyph::allele_tower(3)

NAME | SYNOPSIS | DESCRIPTION | BUGS | SEE ALSO | AUTHOR

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