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

💖 Bio::G...le_box — the manual, but make it cute 💖

okay bestie, so this is a page from the User Contributed Perl Documentation — it's Bio::G...le_box, living in section 3pm of the perl manual, and it's literally the moment your genome-wide data stops being a slow sad mess. 🦋

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✨ NAME ✨

Bio::Graphics::Glyph::wiggle_box — a generic box glyph that's compatible with dense "wig" data. yes, that's the whole vibe. 🎀

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✨ SYNOPSIS ✨

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

that's it. that's the synopsis. she's low maintenance. 💅

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✨ DESCRIPTION ✨

so here's the tea 🍓: this glyph does everything the regular 'box' glyph does, but it also takes value data in Bio::Graphics::Wiggle file format. like, this format:

reference = chr1
ChipCHIP Feature1 1..10000 wigfile=./test.wig;wigstart=0
ChipCHIP Feature2 10001..20000 wigfile=./test.wig;wigstart=656
ChipCHIP Feature3 25001..35000 wigfile=./test.wig;wigstart=1312

the wigfile attribute is the relative or absolute pathname to a Bio::Graphics::Wiggle format file. the optional wigstart option gives the offset to the start of the data. if you don't specify it, a linear search will be used to find the data instead. and the data itself? it's a packed binary representation of the values in the feature, using a constant step — like the kind you see in tiling array data. 📊

this glyph is intended for dense, qualitative feature data. any score data for each data point only gets evaluated for true/false — when true, a box of the specified bgcolor is drawn; when false, nothing is drawn. no data smoothing is used, periodt.

two primary benefits of using this glyph (with wiggle data), bestie:

1. for large, genome-wide data sets, the speed of panel rendering is greatly improved. ⚡
2. large sets of related features can be rendered as a UCSC-style subtrack without the need for aggregation or a GFF3 containment hierarchy. 👑

a disadvantage to this approach is that individual features will have no attributes associated with them and will appear as anonymous blocks within a sub-track. 😭 rip.

an example use for this glyph is annotated transcribed regions from microarray experiments. such regions are identified based on raw microarray data but don't necessarily have a score associated with them. in this case, using the wiggle_box glyph provides a graphical summary of an expression array experiment. 🌈

🌸 DATA 🌸

the wiggle data used for this glyph should be loaded using the 'BED' format, in order to allow features of variable width. the fourth column should be a true value, with numeric or ".". an example is shown below:

track type=wiggle_0 name="transfrags" description="D. melanogaster transcribed fragments 0-2hrs"
2L      9309    9451    1
2L      10697   11021   1
2L      11101   11345   1
2L      11410   11521   1
2L      11771   12243   1
2L      12314   12954   1
2L      13516   15746   1
2L      17033   17191   1
2L      18232   18580   1
2L      19860   19999   1

look at her go. 🧚

🎀 OPTIONS 🎀

this glyph accepts the standard generic option set. it differs in that the label and description and title/mouseover labels apply to the whole, panel-wide sub-track feature rather than to individual boxes. so like, the vibes are collective, not per-box. 🫶

see Bio::Graphics::Glyph::wiggle_xyplot for a description of the wiggle-specific options and data formats. go read that one too, iykyk. 💜

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💀 BUGS 💀

please report them. that's the whole section. she said "no thoughts, just report bugs." 🙈

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⭐ SEE ALSO ⭐

okay here comes the whole friend group, no one gets left out:

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::allele_tower, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD

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👑 AUTHOR 👑

Sheldon McKay <mckays@cshl.edu>. what an icon. 💖

Copyright (c) 2008 Cold Spring Harbor Laboratory

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

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and that's the whole page, bestie 🎀 — this was perl v5.30.0, dated 2019-11-25, and yeah, she's still serving. mwah. 💅✨