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

📦
version 2.40 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🦋 NAME 🦋

okay so this page is about Bio::Graphics::Glyph::vista_plot — the "vista_plot" glyph 💅 and yes she's the main character here.

✨ SYNOPSIS ✨

bestie, the actual deets live in these pages, go peek at them:

  • Bio::Graphics::Glyph
  • Bio::Graphics::Glyph::wiggle_xyplot
  • Bio::Graphics::Glyph::heat_map

🌸 DESCRIPTION 🌸

So this glyph draws peak calls — that's features with discreet boundaries, like putative transcription sites — on top of a signal graph (wiggle_xyplot). But heads up, it needs a special load gff file that uses the attributes wigfile and peak_type. no cap.

Example, literally right here:

2L  chip_seq  vista  5407   23011573  .  .  .  Name=ChipSeq Exp
1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1

The glyph draws the wiggle file first, then overlays the peaks (if there are any) over the signal graph. And elsewhere in the GFF3 file there should be one or more features of type "binding_site:exp1", like:

2L  exp1  binding_site  91934  92005  .  .  .

Options like 'balloon hover' and 'link' are available to customize how you interact with peaks in detail view 🫶

🌈 BigWig support

BigWig format is supported too, but it also requires another attribute supplied in the load gff file (fasta), which specifies the sequence index file for the organism in use. The data file should have the 'bw' extension — that's what vista_plot uses to detect the BigWig format 🎀

3L  chip_seq  vista   1    24543530  .  .  .   Name=ChipSeq Exp
2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta
⚠️ Note that all attributes should be present in load gff, because the code currently does not handle the situation when only some of the attributes are in the gff. To omit peak or signal drawing, use "" (i.e. peak_type="").

In both cases the stanza code will look the same (only essential parameters shown):

 [VISTA_PLOT]
 feature         = vista:chip_seq
 glyph           = vista_plot
 label           = 1
 smoothing       = mean
 smoothing_window = 10
 bump density    = 250
 autoscale       = local
 variance_band   = 1
 max_peak        = 255
 min_peak        = 1
 peakwidth       = 3
 start_color     = lightgray
 end_color       = black
 pos_color       = blue
 neg_color       = orange
 bgcolor         = orange
 alpha           = 80
 fgcolor         = black
 database        = database_with_load_gff_data
 box_subparts    = 1
 bicolor_pivot   = min
 key             = VISTA plot

👑 OPTIONS 👑

Options are the same as for wiggle_xyplot and heat_map 💖

Additional parameters:

  • alpha — sets the transparency for the peak area ✨
  • glyph_subtype — displays only 'peaks', 'signal', 'density' or 'peaks+signal'. Aliases for 'peaks+signal' include "both" and "vista" 💅

Recommended global settings:

for proper peak drawing, transparency should be enabled by setting truecolors=1 in the GBrowse.conf file ⭐

💀 BUGS 💀

Please report them 🙈 (fr, they wanna know)

🧚 SEE ALSO 🧚

  • Bio::Graphics::Panel
  • Bio::Graphics::Glyph
  • Bio::Graphics::Glyph::wiggle_xyplot
  • Bio::Graphics::Glyph::heat_map
  • GD

💜 AUTHOR 💜

Peter Ruzanov pruzanov@oicr.on.ca

Copyright (c) 2010 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.

and that's the whole vibe bestie 🎀 this one's from perl v5.30.0, dated 2019-11-25 — iconic, ate, periodt ✨🦋💖

📦 where this page comes from