PlotPies {FlowSOM} | R Documentation

## Plot comparison with other clustering

### Description

Plot FlowSOM grid or tree, with pies indicating another clustering or manual gating result

### Usage

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

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`cellTypes` | Array of factors indicating the celltypes
`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
`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).
`legend` | Logicle, if T add a legend
`main` | Title of the plot

### Value

Nothing is returned. A plot is drawn in which each node is represented by a pie chart indicating the percentage of cells present of each cell type. At the end, the layout is set to 1 figure again.

### See Also

`PlotStars`,`PlotMarker`, `PlotCenters`,`BuildMST`

### Examples

       # Read from file, build self-organizing map and minimal spanning tree
       fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
       flowSOM_res <- FlowSOM(fileName, compensate=TRUE,transform=TRUE,
                                scale=TRUE,colsToUse=c(9,12,14:18),nClus=7)
       ff <- flowCore::read.FCS(fileName)
       ff_c <- flowCore::compensate(ff,flowCore::description(ff)$SPILL)
       flowCore::colnames(ff_c)[8:18] <- paste("Comp-",
                                         flowCore::colnames(ff_c)[8:18],
                                         sep="")

       # Get the manually gated labels using a gatingML file
       gatingFile <- system.file("extdata","manualGating.xml",
                                 package="FlowSOM")
       gateIDs <- c( "B cells"=8,
                     "ab T cells"=10,
                     "yd T cells"=15,
                     "NK cells"=5,
                     "NKT cells"=6)
       cellTypes <- c("B cells","ab T cells","yd T cells",
                     "NK cells","NKT cells")
       gatingResult <- ProcessGatingML(ff_c, gatingFile, gateIDs, cellTypes)

       # Plot pies indicating the percentage of cell types present in the nodes
       PlotPies(flowSOM_res[[1]],gatingResult$manual)

[Package FlowSOM version 1.12.0 Index]