Provided by: libbio-graphics-perl_2.40-2_all bug


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


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


       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:

        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

        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.

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

         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                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.


       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:

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


       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(<>) {
           my($chr,$start,$stop,$band,$stain) = split /\t/;
           $chr = ucfirst($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;

       foreach my $chr(sort keys %chrom_ends) {
           my $chr_orig = $chr;
           $chr =~ s/chr//i;


       Please report them.


       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


       Gudmundur A. Thorisson <>

       Copyright (c) 2001-2006 Cold Spring Harbor Laboratory


       Sheldon McKay <<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.