RelabelMetaclusters {FlowSOM}R Documentation

RelabelMetaclusters

Description

Adapt the metacluster levels. Can be used to either give them new names, or potentially merge some metaclusters.

Usage

RelabelMetaclusters(fsom, labels)

Arguments

fsom

Result of calling the FlowSOM function

labels

Named vector, with the names the original metacluster names and the values the replacement

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 = 10,
                       seed = 1)
                       
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering)
GetCounts(flowSOM.res)

# Include MC9 in MC8
flowSOM.res <- RelabelMetaclusters(flowSOM.res, c("9" = "8")) 
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering)
GetCounts(flowSOM.res)

# Give different names

flowSOM.res <- RelabelMetaclusters(flowSOM.res, c("1" = "1: CD8+",
                                                  "7" = "7: gd+",
                                                  "8" = "8: CD19+"))
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering)
PlotNumbers(flowSOM.res, level = "metaclusters")
GetCounts(flowSOM.res)


[Package FlowSOM version 2.0.0 Index]