It is useful for "backgating" plots.

geom_overlay(data, ...)



a filter (Currently only rectangleGate (1d or 2d), polygonGate, ellipsoidGate are supported.) or a list of these gates or filterList or character specifying a gated cell population in the GatingSet


other arguments mapping, The mapping aesthetic mapping data a polygonGate fill polygonGate is not filled by default colour default is red pd pData (data.frame) that has rownames represents the sample names used as key to be merged with filterList


a geom_overlay layer


library(ggcyto) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) p <- autoplot(gs, "CD3+")
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
# add a flowSet as the overlay fs <- gs_pop_get_data(gs, "DPT") p + geom_overlay(data = fs, size = 0.3, alpha = 0.7)
# add overlay layer by gate name p + geom_overlay(data = "DNT", size = 0.3, alpha = 0.7)
#add overlay for 1d densityplot p <- ggcyto(gs, aes(x = CD4), subset = "CD3+") + geom_density(aes(y = ..count..)) p + geom_overlay("DNT", aes(y = ..count..), fill = "red")