man Bio::Graphics::Glyph::allele_tower (3): The allele

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.

AUTHOR

Fiona Cunningham <[email protected]> in Lincoln Stein's lab <[email protected]>.