vitessce-r

R API and htmlwidget facilitating interactive visualization of spatial single-cell data with Vitessce.

Installation

Installation requires R 4.0.0 or greater.

install.packages("devtools")
devtools::install_github("vitessce/vitessceR")

Usage

library(vitessceR)

vc <- VitessceConfig$new()
vc$widget()

For full examples, visit the documentation.

For questions and help with using the package, please open a discussion.

Development

npm install
npm run build

setwd("path/to/vitessceR")
install.packages("htmlwidgets")
install.packages("devtools")
devtools::install()
devtools::load_all()

Testing

devtools::check()
devtools::test()

Documentation

install.packages("devtools")
install.packages("pkgdown")
devtools::document()
pkgdown::build_site()

Documentation is automatically deployed to GitHub pages with GitHub actions.

Deployment

Currently, the package is only distributed through GitHub. In the future, we plan to submit the package to CRAN or Bioconductor.

To increment the package version, update it in DESCRIPTION.

Resources

• htmlwidgets: creating a widget
• r leaflet
• R packages
• roxygen2 syntax
• R6
• R6 roxygen2 syntax
• plumber: programmatic usage
• pkgdown
• S4