## ----setup, include = FALSE------------------------------------------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----eval=!exists("SCREENSHOT"), include=FALSE------------------------------------------------------------------------ # SCREENSHOT <- function(x, ...) knitr::include_graphics(x) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE-------------------------------------------------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], iSEEpathways = citation("iSEEpathways")[1] ) ## ----"install", eval = FALSE------------------------------------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("iSEEpathways") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----"citation"------------------------------------------------------------------------------------------------------- ## Citation info citation("iSEEpathways") ## ----"start", message=FALSE, warning=FALSE---------------------------------------------------------------------------- library("iSEEpathways") library("fgsea") library("iSEE") # Example data ---- set.seed(1) 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) } ## ----echo=FALSE, out.width="100%"------------------------------------------------------------------------------------- SCREENSHOT("screenshots/get_started.png", delay=20) ## ----createVignette, eval=FALSE--------------------------------------------------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("iSEEpathways.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("iSEEpathways.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE------------------------------------------------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE------------------------------------------------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))