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https://github.com/vitessce/vitesscer

R API and htmlwidget for Vitessce
https://github.com/vitessce/vitesscer

data-visualization gehlenborglab hidivelab htmlwidget kharchenkolab rstudio-widget single-cell vitessce

Last synced: 2 months ago
JSON representation

R API and htmlwidget for Vitessce

Host: GitHub
URL: https://github.com/vitessce/vitesscer
Owner: vitessce
License: other
Created: 2020-09-30T04:05:35.000Z (over 4 years ago)
Default Branch: main
Last Pushed: 2024-07-26T19:57:59.000Z (6 months ago)
Last Synced: 2024-07-26T21:37:30.582Z (6 months ago)
Topics: data-visualization, gehlenborglab, hidivelab, htmlwidget, kharchenkolab, rstudio-widget, single-cell, vitessce
Language: R
Homepage: https://r-docs.vitessce.io
Size: 49 MB
Stars: 33
Watchers: 5
Forks: 9
Open Issues: 13
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE

Awesome Lists containing this project

README

         

# vitessce-r

![R package version](https://img.shields.io/github/r-package/v/vitessce/vitessceR) [![Vitessce JS dependency version](https://img.shields.io/badge/dynamic/json.svg?url=https%3A%2F%2Fraw.githubusercontent.com%2Fvitessce%2FvitessceR%2Fmain%2Fpackage.json&label=vitessce&query=$.dependencies.vitessce&colorB=blue)](https://github.com/vitessce/vitessce/blob/master/CHANGELOG.md) [![docs](https://img.shields.io/badge/docs-📖-57B4E9.svg)](https://vitessce.github.io/vitessceR/)

R API and htmlwidget facilitating interactive visualization of spatial single-cell data with [Vitessce](https://github.com/vitessce/vitessce).

## Installation

Installation requires R 4.0.0 or greater.

```r

install.packages("devtools")

devtools::install_github("vitessce/vitessceR")

```

## Usage

```r

library(vitessceR)

vc <- VitessceConfig$new()

vc$widget()

```

For full examples, visit the [documentation](https://vitessce.github.io/vitessceR/).

For questions and help with using the package, please open a [discussion](https://github.com/vitessce/vitessceR/discussions).



## Development

```sh

npm install

npm run build

```

```r

setwd("path/to/vitessceR")

install.packages("htmlwidgets")

install.packages("devtools")

devtools::install()

devtools::load_all()

```

## Testing

```r

devtools::check()

devtools::test()

```

## Documentation

```r

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`](https://github.com/vitessce/vitessceR/blob/master/DESCRIPTION#L4).

## Resources

- [htmlwidgets: creating a widget](http://www.htmlwidgets.org/develop_intro.html)

- [r leaflet](https://github.com/rstudio/leaflet)

- [R packages](https://r-pkgs.org/)

- [roxygen2 syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html)

- [R6](https://r6.r-lib.org/index.html)

- [R6 roxygen2 syntax](https://www.tidyverse.org/blog/2019/11/roxygen2-7-0-0/#r6-documentation)

- [plumber: programmatic usage](https://www.rplumber.io/articles/programmatic-usage.html)

- [pkgdown](https://pkgdown.r-lib.org/)

- [S4](http://adv-r.had.co.nz/S4.html)