Bio::Graphics::Glyph::ideogram(3pm)			User Contributed Perl Documentation		       Bio::Graphics::Glyph::ideogram(3pm)

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 $_
"; }

       print "##gff-version 3
"; while(<>) {
	   chomp;
	   my($chr,$start,$stop,$band,$stain) = split /	/;
	   $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	UCSC	cytoband	$start	$stop	.	.	.	Parent=$chr;Name=$chr;Alias=$chr$band;stain=$stain;
/; }

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

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.

perl v5.14.2							    2012-02-20				       Bio::Graphics::Glyph::ideogram(3pm)