GitHub - iSEE/iSEEpathways: iSEE extension for panels related to pathway analysis (original) (raw)

iSEEpathways

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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 fromCRAN. Then install iSEEpathways fromBioconductor using the following code:

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

BiocManager::install("iSEEpathways")

And the development version fromGitHub 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 citeiSEEpathways.

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 aContributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

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 aContributor Code of Conduct. By contributing to this project, you agree to abide by its terms.