FlowSOMmary {FlowSOM} | R Documentation |
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.
FlowSOMmary(fsom, plotFile = "FlowSOMmary.pdf")
fsom |
FlowSOM object, as generated by |
plotFile |
Name of the pdf file that will be generated (default is
FlowSOMmary.pdf). If |
Returns a summary of the FlowSOM object
# 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)