geom_stats {ggcyto}R Documentation

Popluation statistics layer

Description

It is a virtual layer and will be instanatiated as geom_label layer within ggycto.+ operator.

Usage

geom_stats(gate = NULL, ..., value = NULL, type = "percent",
  data_range = NULL, negated = FALSE, adjust = 0.5,
  label.padding = unit(0.05, "lines"), label.size = 0, digits = 3)

Arguments

gate

a 'filterList' or character (represent as a population node in GatingSet) if not supplied, ggcyto then tries to parse the gate from the first geom_gate layer.

...

other arguments passed to geom_label layer

value

the pre-calculated stats value. when supplied, the stats computing is skipped.

type

can be "percent", "count" or "MFI" (MFI is currently not supported yet).

data_range

a data.frame that specifies the data range for each channels (see examples for its format.) Default is the instrument range extracted from fs object.

negated

whether the gate needs to be negated

adjust

adjust the position of the centroid. from 0 to 1.

label.padding, label.size

arguments passed to geom_label layer

digits

control the stats format

Details

So it is dedicated for ggcyto context and thus can't not be added to ggplot object directly.

Value

a geom_popStats layer

Examples

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
# add gate and stats layer
p + geom_gate("CD4") + geom_stats()

#sometime the stats are not shown (or positoned not properly) due to the inaccurate default instrument measurement range
#stored in flow data. then it will be necessary to correct that by supplying the actual 'data_range'
fr <- getData(gs)[[1]]
rng <- range(fr, type = "data")
p + geom_gate("CD4") + geom_stats(data_range = rng)

[Package ggcyto version 1.6.2 Index]