The volcano3D package enables exploration of probes differentially expressed between three groups. Its main purpose is for the visualisation of differentially expressed genes in a three-dimensional volcano plot. These plots can be converted to interactive visualisations using plotly.

The vignette explores a case study from the PEAC rheumatoid arthritis trial (Pathobiology of Early Arthritis Cohort). The methodology has been published in Lewis, Myles J., et al. Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell reports 28.9 (2019): 2455-2470. (DOI: 10.1016/j.celrep.2019.07.091) with an interactive web tool available at https://peac.hpc.qmul.ac.uk.

This tool acts as a searchable interface to examine relationships between individual synovial and blood gene transcript levels and histological, clinical, and radiographic parameters, and clinical response at 6 months. An interactive interface allows the gene module analysis to be explored for relationships between modules and clinical parameters. The PEAC interactive web tool was creating as an R Shiny app and deployed to the web using a server.

There are also supplementary vignettes for further information on:

• Using the volcano3D package to perform 2x3-way analysis. In this type of analysis there is a binary factor such as drug response (responders vs non-responders) and a 2nd factor with 3 classes such as a trial with 3 drugs. See here.
• Using the volcano3D package to create and deploy a shiny app. See here.

## Getting Started

### Install from CRAN

install.packages("volcano3D")

### Install from Github

library(devtools)
install_github("KatrionaGoldmann/volcano3D")
library(volcano3D)

### volcano3D data

The sample data can then also be installed either from source or using:

install_github("KatrionaGoldmann/volcano3Ddata")

## Citation

volcano3D was developed by the bioinformatics team at the Experimental Medicine & Rheumatology department and Centre for Translational Bioinformatics at Queen Mary University London.

If you use this package please cite as:

citation("volcano3D")

##
## To cite package 'volcano3D' in publications use:
##
##   Katriona Goldmann and Myles Lewis (2022). volcano3D: 3D Volcano Plots
##   and Polar Plots for Three-Class Data. R package version 2.0.0.
##   https://CRAN.R-project.org/package=volcano3D
##
## A BibTeX entry for LaTeX users is
##
##   @Manual{,
##     title = {volcano3D: 3D Volcano Plots and Polar Plots for Three-Class Data},
##     author = {Katriona Goldmann and Myles Lewis},
##     year = {2022},
##     note = {R package version 2.0.0},
##     url = {https://CRAN.R-project.org/package=volcano3D},
##   }

or:

Lewis, Myles J., et al. Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell reports 28.9 (2019): 2455-2470.