ReassignMetaclusters {FlowSOM}R Documentation

ReassignMetaclusters

Description

Adapt the metaclustering. Can be used to either split up metaclusters, or potentially merge some metaclusters.

Usage

ReassignMetaclusters(fsom, metaclustering)

Arguments

fsom

Result of calling the FlowSOM function

metaclustering

Vector with the metacluster names for all clusters

Value

Updated FlowSOM object

Examples

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::transformList(colnames(flowCore::keyword(ff)[["SPILL"]]),
                                flowCore::logicleTransform()))
flowSOM.res <- FlowSOM(ff,
                       scale = TRUE,
                       colsToUse = c(9, 12, 14:18), 
                       nClus = 5,
                       seed = 1)
                       
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering)

# Split up metacluster 3
MC_or <- flowSOM.res$metaclustering
MC_new <- c(MC_or)
MC_new[c(81:86, 91:96)] <- "5b"

flowSOM.res <- ReassignMetaclusters(flowSOM.res, MC_new)
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering)
PlotNumbers(flowSOM.res, level = "metaclusters")
GetCounts(flowSOM.res)


[Package FlowSOM version 2.0.0 Index]