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:varThis 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.gzOtherwise 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.
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::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Gudmundur A. Thorisson <mummi@cshl.edu>
Copyright (c) 2001-2006 Cold Spring Harbor Laboratory
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.