ggcyto (version 1.0.5)

geom_gate: add a flowCore gate layer

Description

When 'data' is a gate (or flowCore filter) or a list of gates or a filterList object. When it is used directly with 'ggplot', pdata of the flow data must be supplied through 'pd' argument explicitly in order for the gates to be dispatched to each panel. However It is not necessary when used with 'ggcyto' wrapper since the latter will attach pData automatically.

Usage

geom_gate(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)
"geom_gate"(data, ...)

Arguments

data

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

Value

a geom_gate layer

Details

When 'data' is a character, it construct an abstract geom layer for a character that represents nodes in a Gating tree and will be instanatiated later as a specific geom_gate layer or layers based on the gates extracted from the given GatingSet object.

Examples

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`))
p <- p + geom_hex(bins = 128)
rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)))
#constuctor for a list of filters
rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)
p + geom_gate(rect.gates)

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)
# add gate layer by gate name
p + geom_gate("CD4")