PlotNumbers {FlowSOM} | R Documentation

## Plot the index of each node

### Description

Plot FlowSOM grid or tree, with in each node a number indicating its index

### Usage

    PlotNumbers(
      fsom,
      view = "MST",
      main = NULL,
      nodeSize = fsom$MST$size,
      fontSize = 1,
      backgroundValues = NULL,
      backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
      backgroundLim = NULL,
      backgroundBreaks = NULL
    )

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`view` | Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
`main` | Title of the plot
`nodeSize` | Nodesize. The plot might be easier to read if this is a constant number, e.g. 10 or 15
`fontSize` | Fontsize, passed to label.cex
`backgroundValues` | Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)
`backgroundColor` | Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors
`backgroundLim` | Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.
`backgroundBreaks` | Breaks to pass on to `cut`, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).

### Value

Nothing is returned. A plot is drawn in which each node is assigned a number

### See Also

`PlotMarker`,`PlotStars`, `PlotPies`,`PlotCenters`, `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 the node IDs
    PlotNumbers(flowSOM.res)

    # Adapt node size for easier readability
    PlotNumbers(flowSOM.res, nodeSize=14)

[Package FlowSOM version 1.19.4 Index]