Bio::G...eogram(3pm)

💖 NAME 💖

Bio::Graphics::Glyph::ideogram — the ideogram glyph, bestie. Yes it's a real manual page (perl v5.30.0, dated 2019-11-25, if you were wondering) and yes we're gonna get through all of it together 🫶

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✨ SYNOPSIS ✨

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

Like, that's it. That's the whole synopsis. Go read those two. 💅

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🦋 DESCRIPTION 🦋

Okay so this glyph draws a section of a chromosome ideogram. It's giving science class but make it cute.

It relies on certain data from the feature to figure out:

• which color should be used (that's the stain, bestie),
• and whether the segment is a telomere, a centromere, or just a regular old cytoband.

Here's the tea: the centromeres and the 'var'-marked bands get rendered with diagonal black-on-white patterns if the -patterns option is true. If it's not true? They get rendered in dark gray instead. And no, this isn't just aesthetic — it's literally to prevent a libgd2 crash on certain 64-bit platforms when rendering patterned images 😭 so do not come for the gray, the gray is load-bearing.

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.

🎀 Heads up: that middle bit is one single GFF3 file and one single GBrowse config, so if you're copying it, copy it all — the ..., the URL, and the config block are all part of the same flow.

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🌸 OPTIONS 🌸

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

• -fgcolor — Foreground color. Default: black
• -outlinecolor — Synonym for -fgcolor.
• -linewidth — Line width. Default: 1
• -height — Height of glyph. Default: 10
• -font — Glyph font. Default: gdSmallFont
• -connector — Connector type. Default: 0 (false)
• -connector_color — Connector color. Default: black
• -label — Whether to draw a label. Default: 0 (false)
• -description — Whether to draw a description. Default: 0 (false)

The following options are specific to the ideogram glyph. 👑

• -bgcolor — Band coloring string. Default: none
• -bgfallback — Coloring to use when no bands are present. Default: yellow

-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

So what that's saying is: use "white" for features whose stain attribute is "gneg", "silver" for those whose stain attribute is "gpos25", and so on, and so on, forever and ever amen 💫

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. Slay, simple.

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. 🩹

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🧚 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/;
}

💀 No cap, run it exactly as written. The $stains{$stain} = 1; line is there, the next is there, the \_ escape is there. Don't "clean it up", bestie, that's how the glyph's input gets born.

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😭 BUGS 😭

Please report them. That's it, that's the whole section. Please. Report. Them. 🙏

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🌈 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

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👑 AUTHOR 👑

Gudmundur A. Thorisson <mummi@cshl.edu>

Copyright (c) 2001-2006 Cold Spring Harbor Laboratory

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💜 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.

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And that's the whole page, bestie!! 💖 Written by the perl v5.30.0 era, dated 2019-11-25, and living in the Bio::G...eogram(3pm) slot of your local manual. Go draw a chromosome, you absolute icon. 🎀✨