PlotPies {FlowSOM} | R Documentation |
Plot comparison with other clustering
PlotPies( fsom, cellTypes, colorPalette = grDevices::colorRampPalette(c("white", "#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), ... )
fsom |
FlowSOM object, as generated by |
cellTypes |
Array of factors indicating the celltypes |
colorPalette |
Color palette to use. |
... |
Additional arguments to pass to |
Plot FlowSOM grid or tree, with pies indicating another clustering or manual gating result
Ggplot plot
PlotStars
, PlotVariable
,
PlotFlowSOM
, PlotLabels
,
PlotNumbers
, PlotMarker
,
QueryStarPlot
, PlotSD
# Identify the files fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM") wsp_file <- system.file("extdata", "gating.wsp", package = "FlowSOM") # Specify the cell types of interest for assigning one label per cell cellTypes <- c("B cells", "gd T cells", "CD4 T cells", "CD8 T cells", "NK cells", "NK T cells") # Parse the FlowJo workspace gatingResult <- GetFlowJoLabels(fcs_file, wsp_file, cellTypes = cellTypes) # Check the number of cells assigned to each gate colSums(gatingResult$matrix) # Build a FlowSOM tree flowSOM.res <- FlowSOM(fcs_file, scale = TRUE, compensate = TRUE, transform = TRUE, toTransform = 8:18, colsToUse = c(9, 12, 14:18), nClus = 10, seed = 1) # Plot pies indicating the percentage of cell types present in the nodes PlotPies(flowSOM.res, gatingResult$manual, backgroundValues = flowSOM.res$metaclustering)