compute_stats: compute the statistics of the cell population defined by...

In RGLab/ggcyto: Visualize Cytometry data with ggplot

compute the statistics of the cell population defined by gates

Description

It calls the underlining stats routine and merge it with the label position calculated by stat_position as well as the pData of flowSet.

Usage

compute_stats(fs = NULL, gates, type = "percent", value = NULL, ...)

Arguments

fs	flowSet. can be NULL when precaculated 'value' is provided
gates	a list of filters
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).
value	the pre-calculated stats value. when supplied, the stats computing is skipped.
...	other arguments passed to stat_position function

Details

This function is usually not called directly by user but used by ggcyto when geom_stat layer is added.

Value

a data.table that contains percent and centroid locations as well as pData that used as data for geom_btext layer.

Examples

data(GvHD)
fs <- GvHD[1:4]
rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)), filterId = "P1")
rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)
compute_stats(fs, rect.gates)
compute_stats(fs, rect.gates, type = c("gate_name", "percent"))

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