PlotLabels {FlowSOM} | R Documentation

## Plot a label in each node

### Description

Plot FlowSOM grid or tree, with in each node a label. Especially useful to show metacluster numbers

### Usage

    PlotLabels(fsom, labels, 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`
`labels` | A label for every node
`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 label

### See Also

`PlotNumbers`

### Examples

    # Read from file, build self-organizing map and minimal spanning tree
    fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
    ff <- flowCore::read.FCS(fileName)
    ff <- flowCore::compensate(ff, ff@description$SPILL)
    ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff,
                                                   flowCore::colnames(ff)[8:18]))
    flowSOM.res <- FlowSOM(ff,
                           scale=TRUE,
                           colsToUse=c(9,12,14:18),
                           nClus = 10,
                           seed = 1)

    # Plot the node IDs
    PlotLabels( flowSOM.res$FlowSOM, flowSOM.res$metaclustering, nodeSize=15)

[Package FlowSOM version 1.18.0 Index]