FlowSOM (version 1.0.0)

PlotCenters: Plot cluster centers on a 2D plot

Description

Plot FlowSOM nodes on a 2D scatter plot of the data

Usage

PlotCenters(fsom, marker1, marker2, MST=TRUE)

Arguments

fsom

FlowSOM object, as generated by BuildMST

marker1

Marker to show on the x-axis

marker2

Marker to show on the y-axis

MST

logical. If TRUE, plot tree, else plot grid

Value

of the grid are indicated

See Also

PlotStars,PlotPies,PlotMarker, 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)
    
    # Plot centers
    PlotCenters(flowSOM.res,"FSC-A","SSC-A")
    PlotCenters(flowSOM.res,2,5)