## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, results = "markup", message = FALSE, warning = FALSE) ## ----------------------------------------------------------------------------- library(ncdfFlow) library(flowWorkspace) library(CytoML) dataDir <- system.file("extdata",package="flowWorkspaceData") #load raw FCS fs <- load_cytoset_from_fcs(file.path(dataDir,"CytoTrol_CytoTrol_1.fcs")) gs <- GatingSet(fs) ## ----------------------------------------------------------------------------- #compensate comp <- spillover(fs[[1]])[["SPILL"]] chnls <- colnames(comp) comp <- compensation(comp) gs <- compensate(gs, comp) #transform trans <- flowjo_biexp_trans() trans <- transformerList(chnls, trans) gs <- transform(gs, trans) ## ----warning=FALSE------------------------------------------------------------ library(openCyto) #load the original template for tcell panel tbl <- data.table::fread(system.file("extdata/gating_template/tcell.csv", package = "openCyto")) #modify some paramters to fit the current data range tbl[5, gating_args:= "gate_range = c(1e3, 3e3)"] tbl[c(8,11), gating_args:= "gate_range = c(2e3, 3e3)"] #write the new template to disc gtFile <- tempfile() write.csv(tbl, file = gtFile) ##reload the new template gt <- gatingTemplate(gtFile, autostart = 1L) #run the gating gating(gt, gs) #hide the gates that are not of interest toggle.helperGates(gt, gs) #visualize the gates library(ggcyto) autoplot(gs[[1]]) ## ----------------------------------------------------------------------------- outFile <- tempfile(fileext = ".xml") gatingset_to_cytobank(gs, outFile) ## ----eval=FALSE--------------------------------------------------------------- # outFile <- tempfile(fileext = ".wsp") # gatingset_to_flowjo(gs, outFile)