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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}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# iSEEpathways
<!-- badges: start -->
[](https://github.com/iSEE/iSEEpathways/issues)
[](https://github.com/iSEE/iSEEpathways/pulls)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/iSEE/iSEEpathways/actions)
[](https://app.codecov.io/gh/iSEE/iSEEpathways?branch=main)
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The goal of `iSEEpathways` is to provide panels to facilitate the interactive visualisation of pathway analysis results in `r BiocStyle::Biocpkg("iSEE")` applications.
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `iSEEpathways` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEpathways")
```
And the development version from [GitHub](https://github.com/iSEE/iSEEpathways) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("iSEE/iSEEpathways")
```
## Example
This is a basic example which shows you how to load the package:
```{r example, message=FALSE, warning=FALSE, eval = requireNamespace('iSEEpathways')}
library("iSEEpathways")
library("fgsea")
library("iSEE")
# Example data ----
simulated_data <- simulateExampleData()
pathways_list <- simulated_data[["pathwaysList"]]
features_stat <- simulated_data[["featuresStat"]]
se <- simulated_data[["summarizedexperiment"]]
# fgsea ----
set.seed(42)
fgseaRes <- fgsea(pathways = pathways_list,
stats = features_stat,
minSize = 15,
maxSize = 500)
fgseaRes <- fgseaRes[order(pval), ]
head(fgseaRes)
# iSEE ---
se <- embedPathwaysResults(fgseaRes, se, name = "fgsea", class = "fgsea", pathwayType = "simulated",
pathwaysList = pathways_list, featuresStats = features_stat)
app <- iSEE(se, initial = list(
PathwaysTable(ResultName="fgsea", Selected = "pathway_1350 ", PanelWidth = 6L),
FgseaEnrichmentPlot(ResultName="fgsea", PathwayId = "pathway_1350", PanelWidth = 6L)
))
if (interactive()) {
shiny::runApp(app)
}
```
## Citation
Below is the citation output from using `citation('iSEEpathways')` in R. Please
run this yourself to check for any updates on how to cite __iSEEpathways__.
```{r 'citation', eval = requireNamespace('iSEEpathways')}
print(citation('iSEEpathways'), bibtex = TRUE)
```
Please note that the `iSEEpathways` 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 `iSEEpathways` 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/iSEEpathways) 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')`.
## Code of Conduct
Please note that the iSEEpathways 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.