PlotStars {FlowSOM} | R Documentation

## Plot star charts

### Description

Plot FlowSOM grid or tree, where each node is represented by a star chart indicating median marker values

### Usage

    PlotStars(
      fsom,
      markers = fsom$map$colsUsed,
      view = "MST",
      colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan",
        "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
      starBg = "white",
      backgroundValues = NULL,
      backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
      backgroundLim = NULL,
      backgroundBreaks = NULL,
      backgroundSize = NULL,
      thresholds = NULL,
      legend = TRUE,
      query = NULL,
      range = "all",
      main = ""
    )

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`markers` | Array of markers to use. Default: the markers used to build the tree
`view` | Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
`colorPalette` | Colorpalette to be used for the markers
`starBg` | Background color inside the star circle. Default is "white". Can also be put to "transparent" (as was the case for older versions).
`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).
`backgroundSize` | Size of the background circles. Default 15.
`thresholds` | Optional. Array containing a number for each of the markers to be used as the split between high/low. If provided, the percentage of positive cells is indicated instead of the MFI
`legend` | Logical, if TRUE add a legend
`query` | Show a low/high profile for certain markers in the legend. See also `QueryStarPlot`
`range` | If "all" (default), range is computed on all markers passed, if "one", range is computed on every marker separately. The height of the pie pieces will be computed relative to this range.
`main` | Title of the plot

### Value

Nothing is returned. A plot is drawn in which each node is represented by a star chart indicating the median fluorescence intensities. Resets the layout back to 1 plot at the end.

### See Also

`PlotPies`,`PlotMarker`, `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 stars indicating the MFI of the cells present in the nodes
       PlotStars(flowSOM.res)

[Package FlowSOM version 1.20.0 Index]