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)