Plot cluster centers on a 2D plot

Share:

Description

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

Usage

1
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

Type of visualization, if 1 plot tree, else plot grid

Value

Nothing is returned. A 2D scatter plot is drawn on which the nodes of the grid are indicated

See Also

PlotStars,PlotPies, PlotMarker,BuildMST

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
   # 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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.