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.\"
.IX Title "Bio::Graphics::Glyph::ideogram 3pm"
.TH Bio::Graphics::Glyph::ideogram 3pm "2018-09-21" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Graphics::Glyph::ideogram \- The "ideogram" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
.Ve
.SH "DESCRIPTION"
.IX Header "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 \*(L"\-patterns\*(R" 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.
.PP
The cytobandband features would typically be formatted like this in \s-1GFF3:\s0
.PP
.Vb 6
\& ...
\& 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 \*(Aqchromosome\*(Aq 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.
.Ve
.SS "\s-1OPTIONS\s0"
.IX Subsection "OPTIONS"
The following options are standard among all Glyphs.  See
Bio::Graphics::Glyph for a full explanation.
.PP
.Vb 2
\&  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)
.Ve
.PP
The following options are specific to the ideogram glyph.
.PP
.Vb 2
\&  Option      Description                      Default
\&  \-\-\-\-\-\-      \-\-\-\-\-\-\-\-\-\-\-                      \-\-\-\-\-\-\-
\&
\&  \-bgcolor    Band coloring string             none
\&  
\&  \-bgfallback Coloring to use when no bands    yellow
\&                 are present
.Ve
.PP
\&\fB\-bgcolor\fR is used to map each chromosome band's \*(L"stain\*(R" attribute
into a color or pattern. It is a string that looks like this:
.PP
.Vb 2
\&  gneg:white gpos25:silver gpos50:gray \e
\&  gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var
.Ve
.PP
This is saying to use \*(L"white\*(R" for features whose stain attribute is
\&\*(L"gneg\*(R", \*(L"silver\*(R" for those whose stain attribute is \*(L"gpos25\*(R", and so
on. Several special values are recognized: "\fBstalk\fR\*(L" draws a narrower
gray region and is usually used to indicate an acrocentric
stalk. \*(R"\fBvar\fR\*(L" creates a diagonal black-on-white pattern. \*(R"\fBcen\fR"
draws a centromere.
.PP
If \-bgcolor is just a color name, like \*(L"yellow\*(R", the glyph will ignore
all bands and just draw a filled in chromosome.
.PP
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.
.SH "UCSC TO GFF CONVERSION SCRIPT"
.IX Header "UCSC TO GFF CONVERSION SCRIPT"
The following short script can be used to convert a \s-1UCSC\s0 cytoband annotation file
into \s-1GFF\s0 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:
.PP
.Vb 1
\&  fetchideogram.pl http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz
.Ve
.PP
Otherwise you will need to download the file first. Note the difference between this script
and input data from previous versions of ideogram.pm: \s-1UCSC\s0 annotations are used in place
of \s-1NCBI\s0 annotations.
.PP
#!/usr/bin/perl
.PP
use strict;
my \f(CW%stains\fR;
my \f(CW%centros\fR;
my \f(CW%chrom_ends\fR;
.PP
foreach (@ARGV) {
    if (/^(ftp|http|https):/) {
	\f(CW$_\fR = \*(L"lynx \-\-dump \f(CW$_\fR |gunzip \-c|\*(R";
    } elsif (/\e.gz$/) {
	\f(CW$_\fR = \*(L"gunzip \-c \f(CW$_\fR |\*(R";
    }
    print \s-1STDERR\s0 \*(L"Processing \f(CW$_\fR\en\*(R";
}
.PP
print \*(L"##gff\-version 3\en\*(R";
while(<>)
{
    chomp;
    my($chr,$start,$stop,$band,$stain) = split /\et/;
    \f(CW$start\fR++;
    \f(CW$chr\fR = ucfirst($chr);
    if(!(exists($chrom_ends{$chr})) || \f(CW$chrom_ends\fR{$chr} < \f(CW$stop\fR)
    {
	\f(CW$chrom_ends\fR{$chr} = \f(CW$stop\fR;
    }
    my ($arm) = \f(CW$band\fR =~ /(p|q)\ed+/;
    \f(CW$stains\fR{$stain} = 1;
    if ($stain eq 'acen')
    {
	\f(CW$centros\fR{$chr}\->{$arm}\->{start} = \f(CW$stop\fR;
	\f(CW$centros\fR{$chr}\->{$arm}\->{stop} = \f(CW$start\fR;
	next;
    }
    \f(CW$chr\fR =~ s/chr//i;
    print qq/$chr\etUCSC\etcytoband\et$start\et$stop\et.\et.\et.\etParent=$chr;Name=$chr;Alias=$chr$band;stain=$stain;\en/;
}
.PP
foreach my \f(CW$ch\fRr(sort keys \f(CW%chrom_ends\fR)
{
    my \f(CW$chr_orig\fR = \f(CW$chr\fR;
    \f(CW$chr\fR =~ s/chr//i;
    print qq/$chr\etUCSC\etcentromere\et$centros{$chr_orig}\->{p}\->{stop}\et$centros{$chr_orig}\->{q}\->{start}\et.\et+\et.\etParent=$chr;Name=$chr\e_cent\en/;
}
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "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,
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Gudmundur A. Thorisson <mummi@cshl.edu>
.PP
Copyright (c) 2001\-2006 Cold Spring Harbor Laboratory
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Sheldon McKay <mckays@cshl.edu<gt>
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.