ggcyto_add: overloaded '+' method for ggcyto

In RGLab/ggcyto: Visualize Cytometry data with ggplot

overloaded '+' method for ggcyto

Description

It tries to copy pData from ggcyto object to the gate layers so that the gate layer does not need to have pd to be supplied explicitly by users. It also calculates population statistics when geom_stats layer is added. It supports addition ggcyto layers such as 'ggcyto_par' and 'labs_cyto'.

Usage

e1 + e2

Arguments

e1	An object of class ggcyto or a class inheriting from ggcyto, such as ggcyto_flowSet, ggcyto_GatingSet, or ggcyto_GatingLayout. In the case of ggcyto_GatingLayout, the component of e2 will be added to each subsidiary plot.
e2	A component to add to e1

Value

ggcyto object

Examples

## flowSet
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
p <- ggcyto(fs, aes(x = `FSC-H`, y =  `SSC-H`)) + geom_hex(bins = 128)
#add rectangleGate layer (2d)
rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)))
rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)
p + geom_gate(rect.gates) + geom_stats()

## GatingSet
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+") + geom_hex(bins = 64)
p <- p + geom_gate("CD4") + geom_stats() #plot CD4 gate and it is stats
p
p + axis_x_inverse_trans() #inverse transform the x axis into raw scale

## GatingLayout
#autplot for GatingSet
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
gh <- gs[[1]]
p <- autoplot(gh)
class(p)
# customize the font size of strip text for each ggcyo plots contained in GatingLayout object
p + theme(strip.text = element_text(size = 14))

RGLab/ggcyto documentation built on March 3, 2024, 6:23 p.m.