PlotPies {FlowSOM} | R Documentation |
Plot FlowSOM grid or tree, with pies indicating another clustering or manual gating result
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 = "")
fsom |
FlowSOM object, as generated by |
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 |
legend |
Logicle, if T add a legend |
main |
Title of the plot |
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.
PlotStars
,PlotMarker
,
PlotCenters
,BuildMST
# 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)