| ReassignMetaclusters {FlowSOM} | R Documentation |
Adapt the metaclustering. Can be used to either split up metaclusters, or potentially merge some metaclusters.
ReassignMetaclusters(fsom, metaclustering)
fsom |
Result of calling the FlowSOM function |
metaclustering |
Vector with the metacluster names for all clusters |
Updated FlowSOM object
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)