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# iSEEpathways
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The goal of `iSEEpathways` is to provide panels to facilitate the
interactive visualisation of pathway analysis results in
*[iSEE](https://bioconductor.org/packages/3.18/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
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEpathways")
```
And the development version from
[GitHub](https://github.com/iSEE/iSEEpathways) with:
``` r
BiocManager::install("iSEE/iSEEpathways")
```
## Example
This is a basic example which shows you how to load the package:
``` r
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)
#> pathway pval padj log2err ES NES size
#> 1: pathway_1350 0.0004373110 0.5905978 0.4984931 0.2858201 1.503211 299
#> 2: pathway_4907 0.0005947840 0.5905978 0.4772708 0.3250965 1.599638 178
#> 3: pathway_3983 0.0007509197 0.5905978 0.4772708 0.2558001 1.398213 451
#> 4: pathway_398 0.0008716489 0.5905978 0.4772708 0.2799932 1.477849 305
#> 5: pathway_3359 0.0009809867 0.5905978 0.4550599 -0.3724340 -1.674911 106
#> 6: pathway_1289 0.0009835850 0.5905978 0.4550599 0.3479133 1.638048 124
#> leadingEdge
#> 1: feature_6060,feature_9203,feature_1852,feature_1883,feature_12903,feature_2143,...
#> 2: feature_9265,feature_6286,feature_14879,feature_9600,feature_5335,feature_12205,...
#> 3: feature_495,feature_12466,feature_13128,feature_3069,feature_5278,feature_4248,...
#> 4: feature_6478,feature_2164,feature_922,feature_4298,feature_6585,feature_1633,...
#> 5: feature_3879,feature_2726,feature_6870,feature_6787,feature_9700,feature_693,...
#> 6: feature_6376,feature_12953,feature_8391,feature_3147,feature_7330,feature_11551,...
# 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_3363 ", PanelWidth = 6L),
FgseaEnrichmentPlot(ResultName="fgsea", PathwayId = "pathway_3363", 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
print(citation('iSEEpathways'), bibtex = TRUE)
#> To cite package 'iSEEpathways' in publications use:
#>
#> Rue-Albrecht K (2023). _iSEEpathways: iSEE extension for panels
#> related to pathway analysis_. R package version 0.99.0,
#> <https://github.com/iSEE/iSEEpathways>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {iSEEpathways: iSEE extension for panels related to pathway analysis},
#> author = {Kevin Rue-Albrecht},
#> year = {2023},
#> note = {R package version 0.99.0},
#> url = {https://github.com/iSEE/iSEEpathways},
#> }
```
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 *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.18/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://iSEE.github.io/iSEEpathways) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.18/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.
