PlotMarker {FlowSOM} | R Documentation

## Plot marker values

### Description

Plot FlowSOM grid or tree, coloured by node values for a specific marker

### Usage

    PlotMarker(fsom, marker = NULL, view = "MST", main = NULL,
      colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF",
      "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
      backgroundValues = NULL, backgroundColor = function(n) {
      grDevices::rainbow(n, alpha = 0.3) }, backgroundBreaks = NULL,
      backgroundLim = NULL)

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`marker` | Name or index of marker to plot
`view` | Preferred view, options: "MST" (default), "grid" or "tSNE" (if this option was selected while building the MST)
`main` | Title of the plot
`colorPalette` | Color palette to use
`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
`backgroundBreaks` | Breaks to pass on to `cut`, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).
`backgroundLim` | Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.

### Value

Nothing is returned. A plot is drawn in which each node is coloured depending on its median value for the given marker

### References

This visualization technique resembles SPADE results. M. Linderman, P. Qiu, E. Simonds and Z. Bjornson (). spade: SPADE – An analysis and visualization tool for Flow Cytometry. R package version 1.12.2. http://cytospade.org

### See Also

`PlotStars`,`PlotPies`, `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 one marker
    PlotMarker(flowSOM.res,"FSC-A")

[Package FlowSOM version 1.12.0 Index]