EnhancedVolcano
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see EnhancedVolcano.
Publication-ready volcano plots with enhanced colouring and labeling
Bioconductor version: 3.18
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("EnhancedVolcano")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Software, Transcription |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | ggplot2, ggrepel |
| Imports | methods |
| System Requirements | |
| URL | https://github.com/kevinblighe/EnhancedVolcano |
See More
| 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 |
| 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_1.20.0.tar.gz |
| Windows Binary | EnhancedVolcano_1.20.0.zip |
| macOS Binary (x86_64) | EnhancedVolcano_1.20.0.tgz |
| macOS Binary (arm64) | EnhancedVolcano_1.20.0.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 |