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ReadMe.Rmd
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ReadMe.Rmd
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---
title: "volcano3D package"
author: "Katriona Goldmann"
output: md_document
vignette: >
%\VignetteIndexEntry{volcano3D package}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
```{r setup, include = FALSE, echo = FALSE}
knitr::opts_chunk$set(echo = TRUE,
warning = FALSE,
message = FALSE,
fig.height = 7,
fig.width=7,
fig.align = "center")
library(knitr)
library(kableExtra)
```
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
[](https://cran.r-project.org/package=volcano3D)
[](https://cran.r-project.org/package=volcano3D)
`r paste0("[![", Sys.Date(),"]","(",paste0("https://img.shields.io/badge/last%20git%20commit-", gsub('-', '--', Sys.Date()),"-turquoise.svg"), ")]","(",'https://github.com/KatrionaGoldmann/volcano3D/blob/master/NEWS.md',")")`
[](https://GitHub.com/KatrionaGoldmann/volcano3D/issues/)
[](https://github.com/KatrionaGoldmann/volcano3D/actions/workflows/r.yml/badge.svg)
# volcano3D <img src="logo.png" align="right" alt="" width="200" hspace="20" />
```{r, echo=FALSE}
library(ggplot2)
library(ggpubr)
library(plotly)
library(usethis)
```
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](file:///Users/kgoldmann/Documents/Analyses/volcano_package/volcano3D/docs/articles/Extended_Vignette.html)
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)](https://doi.org/10.1016/j.celrep.2019.07.091)
with an interactive web tool available at
[https://peac.hpc.qmul.ac.uk](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](https://www.rstudio.com/products/shiny/) 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](https://katrionagoldmann.github.io/volcano3D/articles/Vignette_2x3.html).
- Using the volcano3D package to create and deploy a shiny app. See [here](https://katrionagoldmann.github.io/volcano3D/articles/shiny_builder.html).
## Getting Started
### Prerequisites
* [ggplot2](https://cran.r-project.org/package=ggplot2)
* [ggpubr](https://cran.r-project.org/package=ggpubr)
* [plotly](https://cran.r-project.org/package=plotly)
### Install from CRAN
[](https://cran.r-project.org/package=volcano3D)
```{r, eval = FALSE}
install.packages("volcano3D")
```
### Install from Github
[](https://GitHub.com/KatrionaGoldmann/volcano3D/tags/)
```{r, eval = FALSE}
library(devtools)
install_github("KatrionaGoldmann/volcano3D")
library(volcano3D)
```
### volcano3D data
The sample data can then also be installed either from
[source](https://github.com/KatrionaGoldmann/volcano3Ddata) or using:
```{r, eval=FALSE}
install_github("KatrionaGoldmann/volcano3Ddata")
```
## Citation
volcano3D was developed by the bioinformatics team at the
[Experimental Medicine & Rheumatology department](https://www.qmul.ac.uk/whri/emr/)
and [Centre for Translational Bioinformatics](https://www.qmul.ac.uk/c4tb/) at
Queen Mary University London.
If you use this package please cite as:
```{r}
citation("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.