PlotCenters {FlowSOM} | R Documentation

## PlotCenters

### Description

Plot cluster centers on a 2D plot

### 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` | Type of visualization, if 1 plot tree, else plot grid

### Details

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

### 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

       # Read from file, build self-organizing map and minimal spanning tree
       fileName <- system.file("extdata", "68983.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
       plot <- Plot2DScatters(flowSOM.res,
                      channelpairs = list(c("FSC-A","SSC-A")),
                      clusters = list(seq_len(NClusters(flowSOM.res))),
                      maxPoints = 0,
                      plotFile = NULL)

[Package FlowSOM version 2.2.0 Index]