## ---- echo=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set(message = FALSE, warning = FALSE, fig.height= 2, fig.width= 3, fig.show = "hold") ## ------------------------------------------------------------------------ library(openCyto) library(ggcyto) gs <- load_gs(system.file("extdata/gs_bcell_auto", package = "flowWorkspaceData")) ## ------------------------------------------------------------------------ fr <- getData(gs[[2]], "Live") chnl <- "CD3" g <- openCyto:::.mindensity(fr, channels = chnl) autoplot(fr, chnl) + geom_gate(g) autoplot(fr, chnl, "SSC-A") + geom_gate(g) ## ------------------------------------------------------------------------ fr <- getData(gs[[1]], "boundary") chnl <- "FSC-A" g <- openCyto:::.mindensity(fr, channels = chnl) mylimits <- ggcyto_par_set(limits = "instrument") p <- autoplot(fr, chnl) + mylimits p + geom_gate(g) autoplot(fr, chnl, "SSC-A") + geom_gate(g) ## ------------------------------------------------------------------------ g <- openCyto:::.mindensity(fr, channels = chnl, gate_range=c(7e4,1e5), adjust = 1.5) p + geom_gate(g) autoplot(fr, chnl, "SSC-A") + geom_gate(g) ## ------------------------------------------------------------------------ g <- openCyto:::.mindensity(fr, channels = chnl, min = 7e4, max = 1e5) p + geom_gate(g) ## ------------------------------------------------------------------------ fr <- getData(gs[[1]], "lymph") chnl <- "Live" g <- openCyto:::.tailgate(fr, channels = chnl, tol = 0.05) p <- autoplot(fr, chnl) + mylimits p + geom_gate(g) autoplot(fr, chnl, "SSC-A") + geom_gate(g) ## ------------------------------------------------------------------------ g <- openCyto:::.quantileGate(fr, channels = chnl, probs = 0.99) p <- autoplot(fr, chnl) + mylimits p + geom_gate(g) autoplot(fr, chnl, "SSC-A") + geom_gate(g) ## ------------------------------------------------------------------------ fr <- getData(gs[[1]], "root") chnl <- c("FSC-A", "SSC-A") g <- openCyto:::.boundary(fr, channels = chnl, min = c(0, 0), max=c(2.5e5,2.5e5)) p <- autoplot(fr, x = chnl[1], y = chnl[2]) p + geom_gate(g) ## ------------------------------------------------------------------------ fr <- read.FCS(system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")) chnl <- c("FSC-A", "FSC-H") g <- openCyto:::.singletGate(fr, channels = chnl) p <- autoplot(fr, x = chnl[1], y = chnl[2]) p + geom_gate(g) ## ------------------------------------------------------------------------ fr <- getData(gs[[1]], "nonDebris") chnl <- c("FSC-A", "SSC-A") g <- openCyto:::.flowClust.2d(fr, channels = chnl, K=2, target=c(1e5,5e4), quantile=0.95) p <- autoplot(fr, x = chnl[1], y = chnl[2]) + mylimits p + geom_gate(g) ## ------------------------------------------------------------------------ fr <- getData(gs[[1]], "CD19andCD20") chnl <- c("CD38", "CD24") g <- openCyto:::.flowClust.2d(fr, channels = chnl, K=6,transitional=TRUE,target=c(3.5e3,3.5e3), quantile=0.95,translation=0.15, pp_res = NULL) p <- autoplot(fr, x = chnl[1], y = chnl[2]) + mylimits p + geom_gate(g) ## ------------------------------------------------------------------------ gs <- load_gs(system.file("extdata/gs_DC_auto", package = "flowWorkspaceData")) fr <- getData(gs[[2]], "HLADR+") chnl <- c("CD11c", "CD123") p <- autoplot(fr, chnl[1], chnl[2]) g <- openCyto:::.quadGate.tmix(fr, channels = chnl, K = 3, usePrior = "no") p + geom_gate(g)