FlowSOM (version 1.0.0)

PlotMarker: Plot marker values

Description

Plot FlowSOM grid or tree, coloured by node values for a specific marker

Usage

PlotMarker(fsom, marker=NULL, MST=TRUE,main=NULL, colorPalette=colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan","#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")))

Arguments

fsom

FlowSOM object, as generated by BuildMST

marker

Name or index of marker to plot

MST

logical. If TRUE, plot tree, else plot grid

main

Title of the plot

colorPalette

Color palette to use

Value

is coloured depending on its mean value for the given marker

References

This visualization technique resembles SPADE results. M. Linderman, P. Qiu, E. Simonds and Z. Bjornson (). spade: SPADE -- An analysis and visualization tool for Flow Cytometry. R package version 1.12.2. http://cytospade.org

See Also

PlotStars,PlotPies,PlotCenters, 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 one marker
    PlotMarker(flowSOM.res,"FSC-A")