PlotPies: PlotPies

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

PlotPies

Description

Plot comparison with other clustering

Usage

PlotPies(
  fsom,
  cellTypes,
  colorPalette = grDevices::colorRampPalette(c("white", "#00007F", "blue", "#007FFF",
    "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
  ...
)

Arguments

fsom	FlowSOM object, as generated by FlowSOM
cellTypes	Array of factors indicating the celltypes
colorPalette	Color palette to use.
...	Additional arguments to pass to PlotFlowSOM

Details

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

Value

ggplot plot

See Also

PlotStars, PlotVariable, PlotFlowSOM, PlotLabels, PlotNumbers, PlotMarker, QueryStarPlot, PlotSD

Examples

# Identify the files
fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM")
gating_file <- system.file("extdata", "gatingResult.csv", 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")
                
# Load manual labels (e.g. GetFlowJoLabels can be used to extract labels from
# an fcs file)
 
gatingResult <- as.factor(read.csv(gating_file, header = FALSE)[, 1])


# 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,
          backgroundValues = flowSOM.res$metaclustering)
          

saeyslab/FlowSOM documentation built on April 15, 2024, 1:03 p.m.