FlowSOM (version 1.0.0)

UpdateNodeSize: Update nodesize of FlowSOM object

Description

Add size property to the graph based on cellcount for each node

Usage

UpdateNodeSize(fsom, reset=FALSE, logScale=FALSE)

Arguments

fsom

FlowSOM object, as generated by BuildMST

reset

logical. If TRUE, all nodes get the same size

logScale

Logical. Use a log scaling on the cell counts

Value

See Also

BuildMST

Examples

    # Read from file, build self-organizing map and minimal spanning tree
    fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
    flowSOM.res <- ReadInput(fileName, compensate=TRUE,transform=TRUE,
                            scale=TRUE)
    flowSOM.res <- BuildSOM(flowSOM.res,colsToUse=c(9,12,14:18))
    flowSOM.res <- BuildMST(flowSOM.res)
    
    # Give all nodes same size
    flowSOM.res <- UpdateNodeSize(flowSOM.res,reset=TRUE)
    PlotStars(flowSOM.res)
    
    # Node sizes relative to amount of cells assigned to the node
    flowSOM.res <- UpdateNodeSize(flowSOM.res)
    PlotStars(flowSOM.res)