GetCounts {FlowSOM} | R Documentation

## GetCounts

### Description

Get counts of number of cells in clusters or metaclusters

### Usage

    GetCounts(fsom, level = "metaclusters")

### Arguments

`fsom` | FlowSOM object
`level` | Character string, should be either "clusters" or "metaclusters" (default)

### Value

A named vector with the counts

### Examples

    # Read from file, build self-organizing map and minimal spanning tree
    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::estimateLogicle(ff,
                                                   flowCore::colnames(ff)[8:18]))
    flowSOM.res <- FlowSOM(ff,
                           scale = TRUE,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10,
                           seed = 1)
    GetCounts(flowSOM.res)
    GetCounts(flowSOM.res, level = "clusters")

[Package FlowSOM version 2.2.0 Index]