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

💖 NAME 💖

Bio::Graphics::Glyph::wiggle_density — a density plot that's BFFs with dense wig data 🧬✨

Okay so real talk, this lives in the Bio::Graphics::Glyph::wiggle_density package, it's a Perl module (3pm, iykyk), and it's part of the User Contributed Perl Documentation. Slay.

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✨ SYNOPSIS ✨

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

That's it bestie, that's the whole synopsis. Go read those two, they're the blueprint. 🫶

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🌸 DESCRIPTION 🌸

So this glyph does the exact same thing as the regular density glyph, but it eats its value data in Bio::Graphics::Wiggle file format. Like:

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 literally just a relative or absolute pathname pointing at a Bio::Graphics::Wiggle format file. Iconic.

The optional wigstart option hands over the offset to the start of the data. And if you don't give it one? It'll do a linear search to find your data. No cap. The data itself is a packed binary representation of the values in the feature, using a constant step — exactly like the vibe you get in tiling array data. 🧚

🎀 OPTIONS 🎀

Same as the regular graded_segments glyph, except these specific ones get recognized:

• basedir — path. The path used to resolve wigfile and densefile tags that give relative paths. Default is to use the current working directory. Absolute wigfile & densefile paths will not be changed. 💅
• autoscale — "local" or "global". If one or more of the min_score and max_score options are missing, then those values get calculated automatically. This option controls how that calculation goes down. "local" scales values according to the min and max values present in the window being graphed. "global" uses chromosome-wide statistics across the entire wiggle or dense file to find min and max. Choose wisely bestie. 👑
• smoothing — method name. Smoothing method: one of "mean", "max", "min" or "none". ✨
• smoothing_window — integer. Number of values across which the data should be smoothed. 🦋
• bicolor_pivot — name. Where to pivot the two colors when drawing bicolor plots. Options are "mean" and "zero". A numeric value can also be provided. 🌈
• pos_color — color. When drawing bicolor plots, the fill color to use for values that are above the pivot point. 💖
• neg_color — color. When drawing bicolor plots, the fill color to use for values that are below the pivot point. 💜

⭐ SPECIAL FEATURE TAGS ⭐

The glyph expects one or more of these tags (attributes) in the feature it renders:

• wigfile — path name. Path to the Bio::Graphics::Wiggle file for vales. (required) — yes, "vales", that's a typo in the original and I am respectfully preserving it, periodt. 😭
• densefile — path name. Path to a Bio::Graphics::DenseFeature object. (deprecated) 💀
• denseoffset — integer. Integer offset to where the data begins in the Bio::Graphics::DenseFeature file. (deprecated) 💀
• densesize — integer. Integer size of the data in the Bio::Graphics::DenseFeature file. (deprecated) 💀

Heads up: densefile, denseoffset and densesize are all marked deprecated. Don't come for me, I'm just the messenger. 🙈

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🐛 BUGS 🐛

Please report them. (Short, sweet, and honestly a mood. Go tell somebody, bestie. 🫶)

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

That's the whole squad. Go read them all, they're all iconic. 💅✨

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💌 AUTHOR 💌

Lincoln Stein <steinl@cshl.edu>.

Copyright (c) 2007 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 a wrap, bestie 💖 this was perl v5.30.0, dated 2019-11-25, and it lives in Bio::G...ensity(3pm) under User Contributed Perl Documentation. stay hydrated, go plot something gorgeous 🌸✨