---
name: "Bio::Graphics::Glyph::ideogram"
section: "3pm"
platform: "linux"
package: "libbio-graphics-perl"
version: "2.40-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Graphics::Glyph::ideogram"
---

# Bio::Graphics::Glyph::ideogram(3pm)

The "ideogram" glyph

## 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 `$ch`r(sort keys `%chrom_ends`) {\
     my `$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.