iSEEpathways

The goal of iSEEpathways is to provide panels to facilitate the interactive visualisation of pathway analysis results in iSEE applications.

Installation instructions

Get the latest stable R release from CRAN. Then install iSEEpathways from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("iSEEpathways")

And the development version from GitHub with:

BiocManager::install("iSEE/iSEEpathways")

Example

This is a basic example which shows you how to load the package:

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.

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. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.

Code of Conduct

Please note that the iSEEpathways project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.