Quick plot for cytometry data

library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5 & Visit %in% c(5:6))[["name"]]]

flowSet

geom_density layer is used for one-dimensional plot.

autoplot(fs, x = 'FSC-H')

geom_hex layer is added for 2d plot.

autoplot(fs, x = 'FSC-H', y = 'SSC-H', bins = 64)

GatingSet

autoplot(gs, "CD3+", bins = 64)

Here are some default settings applied:

• The instrument range is applied by default (through ggcyto_par_set(limits = "instrument")).
• “CD3” gate is plotted aganst its the parent population: “singlets”."
• Axis labels are inverse transformed through axis_x_inverse_trans/axis_x_inverse_trans.

Multiple gates that share the same parent can be plotted together.

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

GatingHierarchy

Multiple cell populations with their asssociated gates can be plotted in different panels of the same plot.

gh <- gs[[1]]
nodes <- getNodes(gh, path = "auto")[c(3:9, 14)]
nodes

## [1] "singlets"    "CD3+"        "CD4"         "CD4/38- DR+" "CD4/38+ DR+"
## [6] "CD4/38+ DR-" "CD4/38- DR-" "CD8"

autoplot(gh, nodes, bins = 64)

Optionally we can disable default grid.arrange behavior and receive a list of ggplot objects instead and manually arrange these individual ggplot objects.

objs <- autoplot(gh, nodes, bins = 64, arrange = FALSE)
length(objs)

## [1] 4

class(objs[[1]])

## [1] "ggcyto_GatingSet"
## attr(,"package")
## [1] "ggcyto"

class(objs[[2]])

## [1] "ggcyto_GatingSet"
## attr(,"package")
## [1] "ggcyto"