geom_stats: Add a popluation statistics layer to a ggcyto plot.

In RGLab/ggcyto: Visualize Cytometry data with ggplot

Add a popluation statistics layer to a ggcyto plot.

Description

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

Usage

geom_stats(
  gate = NULL,
  ...,
  value = NULL,
  type = "percent",
  negated = FALSE,
  adjust = 0.5,
  location = "gate",
  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	a vector of strings to specify the stats types. can be any or multiple values of "percent", "count", "gate_name", or "MFI" (MFI is currently not supported yet).
negated	whether the gate needs to be negated
adjust	see details for stat_position
location	see details for stat_position
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 cannot 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()

# display gate name
p + geom_gate(c("CD4", "CD8")) + geom_stats(type = "gate_name")
# display gate name and percent
p + geom_gate(c("CD4", "CD8")) + geom_stats(type = c("gate_name", "percent"))

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