NAME

Bio::Graphics::Glyph::turnip_pie_multi - The "turnip_pie_multi" glyph

SYNOPSIS

    See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.

DESCRIPTION

This glyph draws a letter for each allele found at a SNP/pSNP/indel 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 from the HapMap project.

The common options are available (except height which is calculated based on the number of alleles).

GETTING THE ALLELES

To specify the alleles, create a "refallele" attribute and an "alleles" attribute for the feature. There should be at least two such attributes (more for complex polymorphisms where there are two or more variant alleles with respect to the consensus). For example, for a C/T polymorphism, the GFF3 load file should look like:

    rDNA        TURNIP_YS4      pSNP    3430    3430    .       .       .       ID=YS4:pSNP:3430;
Name=YS4:pSNP:3430;refallele=c;alleles=c;alleles=t;acounts=TUR:c 0.904761904761905 38 t 0.0952380952380952 4 42;Parent=gnl|ti|1750944306;

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 polymorphism. If you use this option, the major allele will appear in bold type.

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

Robert Davey <robert.davey@bbsrc.ac.uk<gt>, National Collection of Yeast Cultures, Institute of Food Research, Norwich, UK Copyright (c) 2009 NCYC

Original version by: Albert Vernon Smith <albert.smith@cshl.edu> in Lincoln Stein's lab <steinl@cshl.edu>. Copyright (c) 2003 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.