UpdateMetaclusters {FlowSOM} | R Documentation |
Adapt the metacluster levels. Can be used to rename the metaclusters, split or merge existing metaclusters, add a metaclustering and/or reorder the levels of the metaclustering.
UpdateMetaclusters( fsom, newLabels = NULL, clusterAssignment = NULL, levelOrder = NULL )
fsom |
Result of calling the FlowSOM function. |
newLabels |
Optional. Named vector, with the names the original metacluster names and the values the replacement. Can be used to rename or merge metaclusters. |
clusterAssignment |
Optional. Either a named vector, with the names the cluster numbers (characters) or a vector of length NClusters(fsom). Can be used to assign clusters to existing or new metaclusters. |
levelOrder |
Optional. Vector showing the preferred order of the fsom metacluster levels. |
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 = 10, seed = 1) PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering) GetCounts(flowSOM.res) # Merge MC8 and MC9 flowSOM.res <- UpdateMetaclusters(flowSOM.res, newLabels = c("8" = "8+9", "9" = "8+9")) PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering) GetCounts(flowSOM.res) # Split cluster 24 from metacluster 2 and order the metacluster levels flowSOM.res <- UpdateMetaclusters(flowSOM.res, clusterAssignment = c("24" = "debris?"), levelOrder = c("debris?", as.character(c(1:7)), "8+9", "10")) PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering) PlotNumbers(flowSOM.res, level = "metaclusters") GetCounts(flowSOM.res)