It is useful for "backgating" plots.
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
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library(ggcyto) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) p <- autoplot(gs, "CD3+") # 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")
Loading required package: ggplot2 Loading required package: flowCore Loading required package: ncdfFlow Loading required package: RcppArmadillo Loading required package: BH Loading required package: flowWorkspace As part of improvements to flowWorkspace, some behavior of GatingSet objects has changed. For details, please read the section titled "The cytoframe and cytoset classes" in the package vignette: vignette("flowWorkspace-Introduction", "flowWorkspace") Coordinate system already present. Adding new coordinate system, which will replace the existing one.
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