FlowSOM (version 1.0.0)

PlotStars: Plot star charts

Description

Plot FlowSOM grid or tree, where each node is represented by a star chart indicating mean marker values

Usage

PlotStars(fsom, markers=fsom$map$colsUsed, MST=1, legend=TRUE,  clusters=NULL,main="",colorPalette=colorRampPalette( c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),clusterColorPalette= function(n){rainbow(n,alpha=0.3)})

Arguments

fsom

FlowSOM object, as generated by BuildMST

markers

Array of markers to use. Default: the markers used to build the tree

MST

Numeric. If 1 plot tree, if 2 plot grid, if 3 plot tSNE

legend

logical. Sometimes the position of the legend is not great, so it might be easier to plot without

clusters

optional, clustering of the SOM nodes

main

Title of the plot

colorPalette

Colorpalette to be used

clusterColorPalette

Colorpalette to be used for the metaclusters

Value

by a star chart indicating the mean fluorescence intensities

See Also

PlotPies,PlotMarker,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 stars indicating the MFI of the cells present in the nodes
    PlotStars(flowSOM.res)