## @knitr requirements, echo=FALSE if (!require(flowWorkspaceData)) { stop("Cannot build the vignettes without 'flowWorkspaceData'") } ## @knitr setup, include=FALSE library(knitr) opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", message = FALSE, warning = FALSE) ## @knitr load-flowWorkspace, echo=F library(flowWorkspace) ## @knitr load-xml, eval=TRUE flowDataPath <- system.file("extdata", package = "flowWorkspaceData") wsfile <- list.files(flowDataPath, pattern="manual.xml",full = TRUE) wsfile ## @knitr openWorkspace, eval=F ws <- openWorkspace(wsfile) ## @knitr parseWorkspace, eval=F gs <- parseWorkspace(ws, name= "T-cell", subset =1, isNcdf = TRUE) ## @knitr load_gs_manual, echo = FALSE gs <- load_gs(file.path(flowDataPath,"gs_manual")) ## @knitr plot-manual-GatingHierarchy gh <- gs[[1]] plot(gh) ## @knitr plot-manual-gates, fig.width = 9 plotGate(gh) ## @knitr gatingTemplate, eval = T library(openCyto) library(data.table) gtFile <- system.file("extdata/gating_template/tcell.csv", package = "openCyto") dtTemplate <- fread(gtFile, autostart = 1L) dtTemplate ## @knitr gatingTemplate-nonDebris, eval = T dtTemplate[1,] ## @knitr gatingTemplate-singlets, eval = T dtTemplate[2,] ## @knitr gatingTemplate-lympth, eval = T dtTemplate[3,] ## @knitr gatingTemplate-cd3, eval = T dtTemplate[4,] ## @knitr gatingTemplate-cd4cd8, eval = T dtTemplate[5,] ## @knitr gatingTemplate-expand, echo = F, results = F expanded <- openCyto:::.preprocess_csv(dtTemplate) rownames(expanded) <- NULL ## @knitr gatingTemplate-expand1, echo = F expanded[5:6,] ## @knitr gatingTemplate-expand2, echo = F expanded[7:10,] ## @knitr load-gt, eval = T gt_tcell <- gatingTemplate(gtFile, autostart = 1L) gt_tcell ## @knitr plot-gt, eval = T plot(gt_tcell) ## @knitr load-fcs fcsFiles <- list.files(pattern = "CytoTrol", flowDataPath, full = TRUE) ncfs <- read.ncdfFlowSet(fcsFiles) ncfs ## @knitr compensate compMat <- getCompensationMatrices(gh) ncfs_comp <- compensate(ncfs, compMat) ## @knitr compensate_plot, echo = F, fig.width = 5, fig.height = 5 sub_chnl <- c("V545-A","V450-A") fr <- ncfs[[1]][,sub_chnl] fr_comp <- ncfs_comp[[1]][,sub_chnl] fs <- as(list(fr = fr, fr_comp = fr_comp), "flowSet") #transform data to better visualize the compensation effect fs <- transform(fs, estimateLogicle(fr,sub_chnl)) xyplot(`V545-A`~`V450-A`, fs, smooth = FALSE, xbin =64) ## @knitr transformation, eval = T chnls <- parameters(compMat) transFuncts <- estimateLogicle(ncfs[[1]], channels = chnls) ncfs_trans <- transform(ncfs_comp, transFuncts) ## @knitr transformation_plot, echo = F, fig.width = 5, fig.height = 5 fr <- ncfs_comp[[1]][,sub_chnl[1]] fr_trans <- ncfs_trans[[1]][,sub_chnl[1]] fs <- as(list(fr = fr, fr_trans = fr_trans), "flowSet") densityplot(~`V545-A`, fs, stack = FALSE,scales = list(x=list(relation = "free"))) ## @knitr GatingSet gs <- GatingSet(ncfs_trans) getNodes(gs[[1]]) ## @knitr gating, eval = TRUE gating(gt_tcell, gs) ## @knitr gating_par, eval = FALSE ## gating(gt_tcell, gs, mc.cores=2, parallel_type = "multicore") ## @knitr plot_afterGating plot(gs[[1]]) ## @knitr hideGate, results = "hide" dodesToHide <- c("cd8+", "cd4+" , "cd4-cd8-", "cd4+cd8+" , "cd4+cd8-/HLA+", "cd4+cd8-/CD38+" , "cd4-cd8+/HLA+", "cd4-cd8+/CD38+" , "CD45_neg/CCR7_gate", "cd4+cd8-/CD45_neg" , "cd4-cd8+/CCR7+", "cd4-cd8+/CD45RA+" ) lapply(dodesToHide, function(thisNode)setNode(gs, thisNode, FALSE)) ## @knitr rename, results = "hide" setNode(gs, "cd4+cd8-", "cd4") setNode(gs, "cd4-cd8+", "cd8") ## @knitr plot_afterHiding plot(gs[[1]]) ## @knitr plotGate_autoGate, fig.width = 9 plotGate(gs[[1]])