## ---- echo=FALSE-------------------------------------------------------------- knitr::opts_chunk$set(message = FALSE, warning = FALSE, error = TRUE) ## ----echo=FALSE--------------------------------------------------------------- library(ggcyto) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) ## ----------------------------------------------------------------------------- p <- ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+") # 2d plot p <- p + geom_hex(bins = 64) p ## ----------------------------------------------------------------------------- p + ggcyto_par_set(limits = "instrument") ## ----------------------------------------------------------------------------- myPars <- ggcyto_par_set(limits = list(x = c(0,3.5e3), y = c(-10, 4.1e3))) p <- p + myPars# or xlim(0,3.5e3) + ylim(-10, 4e3) p ## ----------------------------------------------------------------------------- ggcyto_par_default() ## ----------------------------------------------------------------------------- p + geom_gate("CD4") ## ----------------------------------------------------------------------------- p <- p + geom_gate(c("CD4","CD8")) # short for geom_gate("CD8") + geom_gate("CD4") p ## ----------------------------------------------------------------------------- p + geom_stats() + labs_cyto("marker") ## ----------------------------------------------------------------------------- p + geom_stats("CD4") ## ----------------------------------------------------------------------------- p + geom_stats("CD4", type = "count", size = 6, color = "white", fill = "black", adjust = 0.3) ## ----error=T------------------------------------------------------------------ p <- ggcyto(gs, aes(x = CD4, y = CD8)) + geom_hex() + myPars p ## ----------------------------------------------------------------------------- p <- p + geom_gate(c("CD4", "CD8")) p ## ----------------------------------------------------------------------------- p + geom_overlay("CD8/CCR7- 45RA+", col = "black", size = 0.1, alpha = 0.4) ## ----------------------------------------------------------------------------- p <- ggcyto(gs, aes(x = CD4), subset = "CD3+") + geom_density(aes(y = ..count..)) p + geom_overlay("CD8/CCR7- 45RA+", aes(y = ..count..), fill = "red") ## ----------------------------------------------------------------------------- p <- ggcyto(gs, aes(x = 38, y = DR), subset = "CD4") + geom_hex(bins = 64) + geom_gate() + geom_stats() p ## ----------------------------------------------------------------------------- ggcyto(gs, subset = "root", aes(x = CD4, y = CD8)) + geom_hex(bins = 64) + geom_gate("CD4") + myPars ## ----------------------------------------------------------------------------- p + axis_x_inverse_trans() + axis_y_inverse_trans() #add filter (consistent with `margin` behavior in flowViz) # ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+", filter = marginalFilter) + geom_hex(bins = 32, na.rm = T)