PlotSD {FlowSOM} | R Documentation

## Plot SD

### Description

— Function in development, use with caution — Plot FlowSOM grid or tree, coloured by standard deviaton

### Usage

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

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`marker` | If a marker is given, the sd for this marker is shown. Otherwise, the maximum ratio is used.
`view` | Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
`main` | Title of the plot
`colorPalette` | Color palette to use
`symmetric` | Plot colours symmetric around zero
`lim` | Variable limits
`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).

### Details

From suggestion in email: I am currently considering a way to summarize for each node all the SD as one value. After computing the SD matrix (nrow = # nodes, ncol = # markers), I compute the median value per column, then divide the SD matrix by it, and finally take the maximum ratio of each line (aka node). Doing so I got a unique dispersion score per node.

### Value

Nothing is returned. A plot is drawn in which each node is coloured depending on its standard deviation

### 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)

    PlotSD(flowSOM.res)

[Package FlowSOM version 1.20.0 Index]