FlowSOMmary {FlowSOM} | R Documentation

## FlowSOMmary

### Description

This functions plots a summary of a flowSOM object. It includes a table of (meta)cluster data, the flowSOM trees and grid view, the (meta)cluster labels, the markers expression, the file distribution if present, the cluster per metacluster percentage, a t-SNE plot, and the MFI per metacluster.

### Usage

    FlowSOMmary(fsom, plotFile = "FlowSOMmary.pdf")

### Arguments

`fsom` | FlowSOM object, as generated by `FlowSOM`
`plotFile` | Name of the pdf file that will be generated (default is FlowSOMmary.pdf). If `NULL`, a list of ggplots will be returned.

### Value

Returns a summary of the FlowSOM object

### Examples

    # Identify the files
    fcs <- flowCore::read.FCS(system.file("extdata", "68983.fcs",
                                          package = "FlowSOM"))

    # Build a FlowSOM object
    flowSOM.res <- FlowSOM(fcs,
                           scale = TRUE,
                           compensate = TRUE,
                           transform = TRUE,
                           toTransform = 8:18,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10,
                           seed = 1)

    FlowSOMmary(flowSOM.res)

[Package FlowSOM version 2.2.0 Index]