UpdateMetaclusters: UpdateMetaclusters

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

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)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.