R: Plot comparison with other clustering

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.

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)