BuildMST: BuildMST

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

BuildMST

Description

Build Minimal Spanning Tree

Usage

BuildMST(fsom, silent = FALSE, tSNE = FALSE)

Arguments

fsom	FlowSOM object, as generated by BuildSOM
silent	If TRUE, no progress updates will be printed
tSNE	If TRUE, an alternative t-SNE layout is computed as well

Details

Add minimal spanning tree description to the FlowSOM object

Value

FlowSOM object containing MST description

See Also

BuildSOM, PlotStars

Examples

# Read from file, build self-organizing map
fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
flowSOM.res <- ReadInput(fileName, compensate=TRUE, transform = TRUE,
                         scale = TRUE)
flowSOM.res <- BuildSOM(flowSOM.res, colsToUse = c(9, 12, 14:18))

# Build the Minimal Spanning Tree
flowSOM.res <- BuildMST(flowSOM.res)

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.