FlowSOMmary: FlowSOMmary

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

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)

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