| RelabelMetaclusters {FlowSOM} | R Documentation |
Adapt the metacluster levels. Can be used to either give them new names, or potentially merge some metaclusters.
RelabelMetaclusters(fsom, labels)
fsom |
Result of calling the FlowSOM function |
labels |
Named vector, with the names the original metacluster names and the values the replacement |
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$metaclustering)
GetCounts(flowSOM.res)
# Include MC9 in MC8
flowSOM.res <- RelabelMetaclusters(flowSOM.res, c("9" = "8"))
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$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)