UpdateMetaclusters {FlowSOM} | R Documentation

## UpdateMetaclusters

### Description

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.

### Usage

    UpdateMetaclusters(
      fsom,
      newLabels = NULL,
      clusterAssignment = NULL,
      levelOrder = NULL
    )

### Arguments

`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.

### 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)

    # 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)

[Package FlowSOM version 2.2.0 Index]