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

✨ Bio::G...id_plot(3pm) ✨

okay bestie, welcome to Bio::G...id_plot(3pm) — the manual page that's about to make your wiggle plots absolutely iconic 💖 if you're here, you're probably staring down a dual-graph situation and you need someone to explain it like a friend, so let's GO.

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🌸 NAME 🌸

Bio::Graphics::Glyph::hybrid_plot — it's an xyplot plot that draws a dual graph using data from two or more wiggle files per track. yes, two graphs. one track. main character energy fr fr 👑

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🦋 SYNOPSIS 🦋

See Bio::Graphics::Panel, Bio::Graphics::Glyph and Bio::Graphics::Glyph::wiggle_xyplot. that's the whole synopsis, she's short and she knows it 💅

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✨ DESCRIPTION ✨

okay so first things first, and this is important: for full functionality, this glyph requires Bio::Graphics::Glyph::generic. why? because the generic glyph is the one drawing your individual matches for small RNA alignments when you're zoomed all the way in — the high zoom level is specified by semantic zooming in your GBrowse conf file. so like, don't skip that part, it's not optional 🙈

Unlike the regular xyplot, this glyph draws two overlapping graphs using value data in Bio::Graphics::Wiggle file format. like so:

track type=wiggle_0 name="Experiment" description="snRNA seq data"
visibility=pack viewLimits=-2:2 color=255,0,0 altColor=0,0,255
windowingFunction=mean smoothingWindow=16

 2L 400 500 0.5
 2L 501 600 0.5
 2L 601 700 0.4
 2L 701 800 0.1
 2L 800 900 0.1

and then, GFF time:

##gff-version 3

2L      Sample_rnaseq  rnaseq_wiggle 41   3009 . . .
ID=Samlpe_2L;Name=Sample;Note=YourNoteHere;wigfileA=/datadir/track_001.2L.wig;wigfileB=/datadir/track_002.2L.wig

so the wigfileA and wigfileB attributes? they hand over a relative or absolute pathname to Bio::Graphics::Wiggle format files, for two concurrent sets of data. basically these wigfiles are carrying the data on signal intensity (counts) for sequences aligned with genomic regions. 🧬

now here's the vibe difference, and it's the whole point:

• in wigfileA the data are additive — so for each sequence region, the signal is calculated as a sum of signals from overlapping matches (signal).
• in wigfileB the signal represents the maximum value among all sequences (signal quality) aligned with the current region.

and why do you care? because this lets you actually see the difference between accumulated signal from overlapping multiple matches (which may likely be just a noise from products of degradation 💀) and high-quality signal from unique sequences. lowkey genius.

want a third wiggle file? use the attribute wigfileC and so forth. keep going, bestie, the alphabet is right there 🌈

⚠️ It is essential that wigfile entries in gff file do not have score, because score is used to differentiate between data for dual graph and data for matches (individual features visible at higher magnification). like, do not put a score there. do not.

After an update to wiggle_xyplot code, colors for the dual plot are now hard-coded (blue for signal and orange for signal quality). Alpha channel is also handled by wiggle_xyplot code now. so you don't get to pick, and honestly? she ate. 🎀

💖 OPTIONS 💖

In addition to some of the wiggle_xyplot glyph options, the following options are recognized:

• wigfileA (path name) — Path to a Bio::Graphics::Wiggle file for accumulated vales in 10-base bins 📈
• wigfileB (path name) — Path to a Bio::Graphics::Wiggle file for max values in 10-base bins 📉
• fasta (path name) — Path to fasta file to enable BigWig drawing 🧚
• u_method (method name) — Use method of [method name] to identify individual features (like alignment matches) to show at high zoom level. By default it is set to 'match' 👑

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💀 BUGS 💀

Please report them. that's it, that's the bug policy. no notes, just 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::allele_tower, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD. the whole friend group showed up, we love to see it 💜

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🌟 AUTHOR 🌟

Peter Ruzanov <pruzanov@oicr.on.ca>.

Copyright (c) 2008 Ontario Institute for Cancer Research.

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 — perl v5.30.0, dated 2019-11-25, and yeah, that footer still says Bio::G...id_plot(3pm) because she keeps it mysterious 💅✨ now go plot something gorgeous 🦋