marginalFilter: Generate a marginal gate.

In ggcyto: Visualize Cytometry data with ggplot

Description

It simply constructs an boundaryFilter that removes the marginal events. It can be passed directly to ggcyto constructor. See the examples for details.

Usage

marginalFilter(fs, dims, ...)

Arguments

fs	flowSet (not used.)
dims	the channels involved
...	arguments passed to boundaryFilter

Value

an boundaryFilter

Examples

data(GvHD)
fs <- GvHD[1]
chnls <- c("FSC-H", "SSC-H")
#before removign marginal events
summary(fs[, chnls])

# create merginal filter
g <- marginalFilter(fs, chnls)
g

#after remove marginal events
fs.clean <- Subset(fs, g)
summary(fs.clean[, chnls])

#pass the function directly to ggcyto
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
# with marginal events
ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+") + geom_hex(bins = 64)

# using marginalFilter to remove these events
ggcyto(gs, aes(x = CD4, y = CD8), subset = "CD3+", filter = marginalFilter) + geom_hex(bins = 64)

ggcyto documentation built on Nov. 8, 2020, 5:30 p.m.