GetPercentages: GetPercentages

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

GetPercentages

Description

Get percentages of number of cells in clusters or metaclusters

Usage

GetPercentages(fsom, level = "metaclusters")

Arguments

fsom	FlowSOM object
level	Character string, should be either "clusters" or "metaclusters" (default) or abbreviations.

Value

A named vector with the percentages

Examples

# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
ff <- flowCore::read.FCS(fileName)
ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]])
ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff,
                                               flowCore::colnames(ff)[8:18]))
flowSOM.res <- FlowSOM(ff,
                       scale = TRUE,
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10,
                       seed = 1)
GetPercentages(flowSOM.res)                      
GetPercentages(flowSOM.res, level = "clusters")

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.