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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
library(BiocStyle)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# iSEEindex
<!-- badges: start -->
[](https://github.com/iSEE/iSEEindex/issues)
[](https://github.com/iSEE/iSEEindex/pulls)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/iSEE/iSEEindex/actions)
[](https://app.codecov.io/gh/iSEE/iSEEindex?branch=main)
<!-- badges: end -->
The goal of `r Biocpkg("iSEEindex")` is to provide an interface to any collection of data sets, hosted anywhere, within a single iSEE web-application.
The main functionality of this package is to define a custom landing page for iSEE web-applications where app maintainers can list entirely custom collections of data sets hosted on virtually any locally or remotely accessible network.
A number of built-in methods are implemented, providing access to common types of resources, e.g.:
- Local filesystem
- HTTPS URIs
- Amazon S3 buckets
- Arbitrary R code to load objects directly
Each type of resource is identified by the scheme component of its URI.
Standard schemes can be used alongside custom-made ones, e.g.:
- `localhost://` for local files.
- `https://` for files downloaded over the HTTPS protocol.
- `s3://` for files downloaded from Amazon S3 buckets.
- `runr://` to load objects directly via a call to R code
The `r Biocpkg("iSEEindex")` framework enables app maintainers to independently define new methods for their own choice of standard and custom-made URI schemes.
More information is available in the vignette *Implementing custom iSEEindex resources*.
The resulting landing page presents end-users of the web-applications with the predefined choice of data sets and initial configuration states (specific to each data set).
After selecting a data set and -- optionally -- an initial configuration, launching the main app fetches resources from their respective URI and caches them using the `r BiocStyle::Biocpkg("BiocFileCache")` package.
Finally, data sets and configurations are loaded from the cache into the main `iSEE` application, for interactive exploration.
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `r Biocpkg("iSEEindex")` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEindex")
```
And the development version from [GitHub](https://github.com/iSEE/iSEEindex) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("iSEE/iSEEindex")
```
## Example
This is a basic example which shows you how to launch an application that lists publicly available data sets hosted on [zenodo.org][zenodo-repository]:
```{r example, eval = requireNamespace('iSEEindex'), message=FALSE, warning=FALSE}
library("iSEEindex")
library("BiocFileCache")
bfc <- BiocFileCache(cache = tempdir())
dataset_fun <- function() {
x <- yaml::read_yaml(system.file(package = "iSEEindex", "example.yaml"))
x$datasets
}
initial_fun <- function() {
x <- yaml::read_yaml(system.file(package = "iSEEindex", "example.yaml"))
x$initial
}
app <- iSEEindex(bfc, dataset_fun, initial_fun)
if (interactive()) {
shiny::runApp(app, port = 1234)
}
```
## Citation
Below is the citation output from using `citation('iSEEindex')` in R. Please
run this yourself to check for any updates on how to cite __iSEEindex__.
```{r 'citation', eval = requireNamespace('iSEEindex')}
print(citation('iSEEindex'), bibtex = TRUE)
```
Please note that the `r Biocpkg("iSEEindex")` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
## Code of Conduct
Please note that the `r Biocpkg("iSEEindex")` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
## Development tools
* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://isee.github.io/iSEEindex) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
<!-- Links -->
[zenodo-repository]: https://zenodo.org/record/7304331