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

💖 NAME 💖

Bio::Graphics::Glyph::wiggle_xyplot — it's giving xyplot but for dense "wig" data, bestie ✨

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🌸 SYNOPSIS 🌸

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

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🦋 DESCRIPTION 🦋

okay so listen. This glyph? It does literally everything the regular xyplot does, except it eats value data in Bio::Graphics::Wiggle file format. iconic behavior fr fr 💅

 reference = chr1
 ChipCHIP Feature1 1..10000 wigfile=./test.wig
 ChipCHIP Feature2 10001..20000 wigfile=./test.wig
 ChipCHIP Feature3 25001..35000 wigfile=./test.wig

The wigfile attribute hands over a relative or absolute pathname pointing at a Bio::Graphics::Wiggle format file. The data in there is a packed binary representation of the values in the feature, using a constant step like the one you'd see in tiling array data. Wigfiles get created with the Bio::Graphics::Wiggle module or the wiggle2gff3.pl script — and both of those are currently part of the gbrowse package, no cap 🌈

Alternatively (because we love options 💁‍♀️), you can just drop an array of quantitative data straight into the wigdata attribute. That can be either:

• an arrayref of quantitative data that starts at feature start and ends at feature end, or
• the data string returned by Bio::Graphics::Wiggle->export_to_wif64($start,$end).

The glyph also supports features that offer a statistical_summary() method, like the ones from Bio::DB::BigWig. That method returns a hash of values — including validCount, maxVal, minVal, sumData, and sumSquares. For each interval, a statistical score gets generated from those values, and the mean, minimum, maximum, or sum of the values may be reported. slay 🎀

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✨ OPTIONS ✨

On top of ALL the xyplot glyph options (every single one, not skipping any), these ones are recognized too:

• basedir — path. The path used to resolve the wigfile and densefile tags when they give relative paths. Default is to use the current working directory. Absolute wigfile & densefile paths? Not changed, periodt 💅
• autoscale — "local" or "global". If one or more of the min_score and max_score options are absent, then these values get calculated automatically. The autoscale option controls how that calculation goes down. The "local" value scales values according to the minimum and maximum values present in the window being graphed. "global" uses chromosome-wide statistics for the entire wiggle or dense file to find the min and max values. 🌍
• smoothing — method name. The smoothing method, bestie. One of "mean", "max", "min" or "none".
• smoothing_window — integer. The number of values across which the data should be smoothed.
• variance_band — boolean. If true, draw a grey band across the entire plot showing the mean and +/- 1 standard deviation (for wig files only, iykyk).
• 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. ⬇️
• interval_method — method. When working with bigWig features that use the statistical_summary() method, this defines the method for reporting one or more scores within each interval. Options include "mean", "sum", "min", or "max". Default is "mean". 💫

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🎀 SPECIAL FEATURE TAGS 🎀

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

• wigfile — path name. Path to the Bio::Graphics::Wiggle file or object for quantitative values. 📁
• wigdata — string. Data exported from a Bio::Graphics::Wiggle in WIF format using its export_to_wif64() method.
• 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 ⚠️).

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💀 BUGS 💀

Please report them. (like, actually please, we're begging 🙏)

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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

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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 the whole vibe bestie 💖 this page came to you courtesy of perl v5.30.0, dated 2019-11-25, filed under Bio::G..._xyplot(3pm) — go forth and plot, you absolute main character 🦋✨