Introduction | Installation | 1. Download the package from Bioconductor | 2. Load the package into R session | Quick start | Plot the most basic volcano plot | Advanced features | Modify cut-offs for log2FC and P value; specify title; adjust point and label size | Adjust colour and alpha for point shading | Adjust shape of plotted points | Adjust cut-off lines and add extra threshold lines | Adjust legend position, size, and text | Fit more labels by adding connectors | Only label key variables | Draw labels in boxes | Italicise labels and flip volcano on it's side | Over-ride colouring scheme with custom key-value pairs | Over-ride colour and/or shape scheme with custom key-value pairs | Encircle / highlight certain variables | Highlighting key variables via custom point sizes | Change to continuous colour scheme | Custom axis tick marks | Acknowledgments | Session info | References
Package: EnhancedVolcano 1.31.0
Jared Andrews
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
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.
Authors:
EnhancedVolcano_1.31.0.tar.gz
EnhancedVolcano_1.31.0.zip(r-4.7)EnhancedVolcano_1.31.0.zip(r-4.6)EnhancedVolcano_1.31.0.zip(r-4.5)
EnhancedVolcano_1.31.0.tgz(r-4.6-any)EnhancedVolcano_1.31.0.tgz(r-4.5-any)
EnhancedVolcano_1.31.0.tar.gz(r-4.7-any)EnhancedVolcano_1.31.0.tar.gz(r-4.6-any)
EnhancedVolcano_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EnhancedVolcano/json (API)
| # Install 'EnhancedVolcano' in R: |
| install.packages('EnhancedVolcano', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kevinblighe/enhancedvolcano/issues
On BioConductor:EnhancedVolcano-1.31.0(bioc 3.24)EnhancedVolcano-1.30.0(bioc 3.23)
rnaseqgeneexpressiontranscriptiondifferentialexpressionimmunooncology
Last updated from:ac469cfa36. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 231 | ||
| linux-devel-x86_64 | NOTE | 274 | ||
| source / vignettes | OK | 354 | ||
| linux-release-x86_64 | NOTE | 268 | ||
| macos-release-arm64 | NOTE | 124 | ||
| macos-oldrel-arm64 | NOTE | 198 | ||
| windows-devel | NOTE | 560 | ||
| windows-release | NOTE | 611 | ||
| windows-oldrel | NOTE | 540 | ||
| wasm-release | OK | 215 |
Exports:EnhancedVolcanogeom_encircleGeomEncircle
Dependencies:clicpp11farverggplot2ggrepelgluegtableisobandlabelinglifecycleR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Publication-ready volcano plots with enhanced colouring and labeling. | EnhancedVolcano |
| Automatically enclose points in a polygon | geom_encircle |
| Custom Geom for Encircling Points in ggplot2 | GeomEncircle |
