## ---- echo=FALSE--------------------------------------------------------- knitr::opts_chunk$set(message = FALSE, warning = FALSE) ## ------------------------------------------------------------------------ library(ggcyto) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_bcell_auto",full = TRUE)) data(GvHD) fs <- GvHD[subset(pData(GvHD), Patient %in%5 & Visit %in% c(5:6))[["name"]]] ## ------------------------------------------------------------------------ autoplot(fs, x = 'FSC-H') ## ------------------------------------------------------------------------ autoplot(fs, x = 'FSC-H', y = 'SSC-H', bins = 64) ## ------------------------------------------------------------------------ autoplot(fs[[1]]) + labs_cyto("marker") ## ------------------------------------------------------------------------ autoplot(gs, "CD3", bins = 64) ## ------------------------------------------------------------------------ autoplot(gs, c("CD3", "CD19"), bins = 64) ## ---- fig.width = 4, fig.height=3---------------------------------------- gh <- gs[[1]] nodes <- getNodes(gh, path = "auto")[c(3:6)] nodes autoplot(gh, nodes, bins = 64) ## ---- fig.width = 8, fig.height=3---------------------------------------- # get ggcyto_GatingLayout object from first sample res <- autoplot(gs[[1]], nodes, bins = 64) class(res) # arrange it as one-row gtable object gt <- ggcyto_arrange(res, nrow = 1) gt # do the same to the second sample gt2 <- ggcyto_arrange(autoplot(gs[[2]], nodes, bins = 64), nrow = 1) # combine the two and print it on the sampe page gt3 <- gridExtra::gtable_rbind(gt, gt2) plot(gt3)