Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
20
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

last update: January 26, 2019

EnhancedVolcano

EnhancedVolcano has now been updated to v1.1.3 (devel). The function was well received here on Biostars (primarily here: A: Volcano plot help code ), which originally gave me the impetus to go for a Bioconductor submission.

CHANGES IN VERSION 1.1.3

  • changed 'colOverride' to 'colCustom'
  • added a new 'shape' parameter to control the shape of plotted points
  • added a new 'shapeCustom' parameter, akin to functionality supplied by 'colCustom' (formerly 'colOverride')
  • added functionality to add title, subtitle, and caption (parameters: title, subtitle, caption, titleLabSize, subtitleLabSize, captionLabSize = 12)
  • added functionality to add extra vertical and horizontal lines (parameters: hline, hlineType, hlineCol, hlineWidth, vline, vlineType, vlineCol, vlineWidth)
  • changed 'colConnectors' default from "black" to "grey10"
  • added extra parameters for line connectors (parameters: typeConnectors, endsConnectors, lengthConnectors)
  • 'labhjust' and 'labvjust' are now 'transcriptLabhjust' and 'transcriptLabvjust', respectively
  • user can now specify to draw transcript labels as text and text in boxes via 'boxedlabels' (TRUE/FALSE)

INSTALLATION

Devel (catch most recent changes):

devtools::install_github('kevinblighe/EnhancedVolcano')

Release (takes time for changes to update):

BiocManager::install('EnhancedVolcano')

---------------------------------------------

ex12-1 ex10-1 ex13-1

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GitHub

https://github.com/kevinblighe/EnhancedVolcano

Bioconductor

https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html

Vignette

https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html


Should anyone wish to provide feedback and / or suggestions for future development, please do so. Credit will always be given where it is due.

Kevin

ADD COMMENTlink modified 20 days ago • written 5 months ago by Kevin Blighe37k
1

Great tool, thanks for putting it together!

My DEseqDataSet is actually a set of peaks instead of transcripts that all have a unique identifier going out to 6 figures, I was wondering if there was a way to use selectLab() to create custom labels such as TF names for factors I know to bind within those peaks or even small representations of their PWMs - though the former would be sufficient for the moment - or does that have to come from an additional metadata column in DEseqDataSet? Thanks!

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by rbronste230
2

Hey, thanks for the comments. My colleague Myles back in London deserves the credit for the initial idea of putting this together. selectLab() will just match up to whatever you have passed to the required lab parameter. So, it can be anything really, but there is no functionality to automatically pull in TF names. That is a good idea, though, and it would show in a nice way which TFs were up- or down-regulated.

I mean, this package is only released for a few weeks at this stage, and I'm fairly open as to where it could be developed further. I was hoping to build something as comprehensive as the ComplexHeatmap package.

ADD REPLYlink written 11 weeks ago by Kevin Blighe37k

and i already used it....

ADD REPLYlink written 5 months ago by krushnach80460
1

Good work dude!

ADD REPLYlink written 5 months ago by Kevin Blighe37k

Hi Kevin,

Great tool! I've been pretty much using it for all my volcano plots. I wanted to know if there was a way to use EnhancedVolcanos with results from sleuth?

cheers!

ADD REPLYlink written 25 days ago by unawaz40

You're welcome. Yes, most likely there is a way. What are the columns in the output of Sleuth?

ADD REPLYlink written 25 days ago by Kevin Blighe37k

This is the output for sleuth, where b is equivalent to Log2FC

ens_gene ext_gene target_id pval qval b se_b mean_obs var_obs tech_var sigma_sq smooth_sigma_sq final_sigma_sq

ADD REPLYlink modified 25 days ago • written 25 days ago by unawaz40

Hey, well, you have at least 2 required columns:

  • ens_gene (label)
  • pval (y)

What is missing is the fold-change for x! I have never used Sleuth, however, I searched the Web forums and am surprised to see that the Sleuth developers do not output a fold-change for Sleuth's results. You may consider using a different differential expression analysis program.

ADD REPLYlink modified 25 days ago • written 25 days ago by Kevin Blighe37k

That's unfortunate. Thanks for looking though!

ADD REPLYlink written 24 days ago by unawaz40

You could likely still use the b value, in which case you should change the x-axis label too. You may want to read through this thread on Google Groups: https://groups.google.com/forum/#!topic/kallisto-sleuth-users/kWodd7CQejE (Harold Pimentel is Sleuth developer)

ADD REPLYlink written 24 days ago by Kevin Blighe37k
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