NAME

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

SYNOPSIS

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

DESCRIPTION

This glyph draws a section of a chromosome ideogram. It relies on certain data from the feature to determine which color should be used (stain) and whether the segment is a telomere or centromere or a regular cytoband. The centromeres and 'var'-marked bands are rendered with diagonal black-on-white patterns if the "-patterns" option is true, otherwise they are rendered in dark gray. This is to prevent a libgd2 crash on certain 64-bit platforms when rendering patterned images.

The cytobandband features would typically be formatted like this in GFF3:

 ...
 ChrX    UCSC    cytoband        136700001       139000000       .       .       .       Parent=ChrX;Name=Xq27.1;Alias=ChrXq27.1;stain=gpos75;
 ChrX    UCSC    cytoband        139000001       140700000       .       .       .       Parent=ChrX;Name=Xq27.2;Alias=ChrXq27.2;stain=gneg;
 ChrX    UCSC    cytoband        140700001       145800000       .       .       .       Parent=ChrX;Name=Xq27.3;Alias=ChrXq27.3;stain=gpos100;
 ChrX    UCSC    cytoband        145800001       153692391       .       .       .       Parent=ChrX;Name=Xq28;Alias=ChrXq28;stain=gneg;
 ChrY    UCSC    cytoband        1       1300000 .       .       .       Parent=ChrY;Name=Yp11.32;Alias=ChrYp11.32;stain=gneg;
 which in this case is a GFF-ized cytoband coordinate file from UCSC:
 http://hgdownload.cse.ucsc.edu/goldenPath/hg16/database/cytoBand.txt.gz
 and the corresponding GBrowse config options would be like this to 
 create an ideogram overview track for the whole chromosome:
 The 'chromosome' feature below would aggregated from bands and centromere using the default 
 chromosome aggregator
 [CYT:overview]
 feature       = chromosome
 glyph         = ideogram
 fgcolor       = black
 bgcolor       = gneg:white gpos25:silver gpos50:gray 
                 gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var
 arcradius     = 6
 height        = 25
 bump          = 0
 label         = 0
 A script to reformat UCSC annotations to  GFF3 format can be found at
 the end of this documentation.

OPTIONS

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.

  Option      Description                      Default
  ------      -----------                      -------
  -fgcolor      Foreground color               black
  -outlinecolor Synonym for -fgcolor
  -linewidth    Line width                     1
  -height       Height of glyph                10
  -font         Glyph font                     gdSmallFont
  -connector    Connector type                 0 (false)
  -connector_color
                Connector color                black
  -label        Whether to draw a label        0 (false)
  -description  Whether to draw a description  0 (false)

The following options are specific to the ideogram glyph.

  Option      Description                      Default
  ------      -----------                      -------
  -bgcolor    Band coloring string             none
  
  -bgfallback Coloring to use when no bands    yellow
                 are present

-bgcolor is used to map each chromosome band's "stain" attribute into a color or pattern. It is a string that looks like this:

  gneg:white gpos25:silver gpos50:gray \
  gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var

This is saying to use "white" for features whose stain attribute is "gneg", "silver" for those whose stain attribute is "gpos25", and so on. Several special values are recognized: "stalk" draws a narrower gray region and is usually used to indicate an acrocentric stalk. "var" creates a diagonal black-on-white pattern. "cen" draws a centromere.

If -bgcolor is just a color name, like "yellow", the glyph will ignore all bands and just draw a filled in chromosome.

If -bgfallback is set to a color name or value, then the glyph will fall back to the indicated background color if the chromosome contains no bands.

UCSC TO GFF CONVERSION SCRIPT

The following short script can be used to convert a UCSC cytoband annotation file into GFF format. If you have the lynx web-browser installed you can call it like this in order to download and convert the data in a single operation:

  fetchideogram.pl http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz

Otherwise you will need to download the file first. Note the difference between this script and input data from previous versions of ideogram.pm: UCSC annotations are used in place of NCBI annotations.

#!/usr/bin/perl

use strict; my %stains; my %centros; my %chrom_ends;

foreach (@ARGV) {
if (/^(ftp|http|https):/) { $_ = "lynx --dump $_ |gunzip -c|";
} elsif (/\.gz$/) { $_ = "gunzip -c $_ |";
}
print STDERR "Processing $_\n"; }

print "##gff-version 3\n"; while(<>) {
chomp;
my($chr,$start,$stop,$band,$stain) = split /\t/;
$start++;
$chr = ucfirst($chr);
if(!(exists($chrom_ends{$chr})) || $chrom_ends{$chr} < $stop)
{ $chrom_ends{$chr} = $stop;
}
my ($arm) = $band =~ /(p|q)\d+/;
$stains{$stain} = 1;
if ($stain eq 'acen')
{ $centros{$chr}->{$arm}->{start} = $stop; $centros{$chr}->{$arm}->{stop} = $start; next;
}
$chr =~ s/chr//i;
print qq/$chr\tUCSC\tcytoband\t$start\t$stop\t.\t.\t.\tParent=$chr;Name=$chr;Alias=$chr$band;stain=$stain;\n/; }

foreach my $chr(sort keys %chrom_ends) {
my $chr_orig = $chr;
$chr =~ s/chr//i;
print qq/$chr\tUCSC\tcentromere\t$centros{$chr_orig}->{p}->{stop}\t$centros{$chr_orig}->{q}->{start}\t.\t+\t.\tParent=$chr;Name=$chr\_cent\n/; }

BUGS

Please report them.

AUTHOR

Gudmundur A. Thorisson <mummi@cshl.edu>

CONTRIBUTORS

Sheldon McKay <mckays@cshl.edu<gt>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

2019-11-25

perl v5.30.0