Ubuntu Manpage: Bio::Graphics::Glyph::ideogram

Provided by: libbio-graphics-perl_2.40-6_all

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>

       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.