library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")

1: suppoort 3 types of plot constructor

  • represent different levels of complexity and flexibility
  • meet the needs of various plot applications
  • suitable for users at different levels of coding skills.

low level: ggplot

The overloaded fority methods empower ggplot to work with all the major Cytometry data structures right away, which allows users to do all kinds of highly customized and versitled plots.

GatingSet

gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
attr(gs, "subset") <- "CD3+"
ggplot(gs, aes(x = `<B710-A>`, y = `<R780-A>`)) + geom_hex(bins = 128) + scale_fill_gradientn(colours = gray.colors(9))

flowSet/ncdfFlowSet/flowFrame

fs <- getData(gs, "CD3+")
ggplot(fs, aes(x = `<B710-A>`)) + geom_density(fill = "blue", alpha= 0.5)

gates

gates <- filterList(getGate(gs, "CD8"))
ggplot(gs, aes(x = `<B710-A>`, y = `<R780-A>`)) + geom_hex(bins = 128) + geom_polygon(data = gates, fill = "transparent", col = "purple")

medium level: ggcyto

ggcyto constructor along with overloaded + operator encapsulate lots of details that might be tedious and intimidating for many users.

ggcyto(gs, aes(x = CD4, y = CD8)) + geom_hex(bins = 128) + geom_gate("CD8")

It simplies the plotting by: * add a default scale_fill_gradientn for you * fuzzy-matching in aes by either detector or fluorochromes names * determine the parent popoulation automatically * exact and plot the gate object by simply referring to the child population name

top level: autoplot

Inheriting the spirit from ggplot’s Quick plot, it further simply the plotting job by hiding more details from users and taking more assumptions for the plot.

  • when plotting flowSet, it determines geom type automatically by the number of dim supplied
  • for GatingSet, it further skip the need of dim by guessing it from the children gate
#1d
autoplot(fs, "CD4")

#2d
autoplot(fs, "CD4", "CD8", bins = 64)

autoplot(gs, c("CD4", "CD8"), bins = 64)