EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling

Bioconductor version: Release (3.20)

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Author: Kevin Blighe [aut, cre], Sharmila Rana [aut], Emir Turkes [ctb], Benjamin Ostendorf [ctb], Andrea Grioni [ctb], Myles Lewis [aut]

Maintainer: Kevin Blighe <kevin at clinicalbioinformatics.co.uk>

Citation (from within R, enter citation("EnhancedVolcano")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EnhancedVolcano")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EnhancedVolcano")

Publication-ready volcano plots with enhanced colouring and labeling	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Software, Transcription
Version	1.24.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	GPL-3
Depends	ggplot2, ggrepel
Imports	methods
System Requirements
URL	https://github.com/kevinblighe/EnhancedVolcano

Suggests	ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	ExpHunterSuite, TOmicsVis
Suggests Me	rliger
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	EnhancedVolcano_1.24.0.tar.gz
Windows Binary (x86_64)	EnhancedVolcano_1.24.0.zip
macOS Binary (x86_64)	EnhancedVolcano_1.24.0.tgz
macOS Binary (arm64)	EnhancedVolcano_1.23.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EnhancedVolcano
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EnhancedVolcano
Bioc Package Browser	https://code.bioconductor.org/browse/EnhancedVolcano/
Package Short Url	https://bioconductor.org/packages/EnhancedVolcano/
Package Downloads Report	Download Stats