PlotPies: PlotPies

View source: R/5_plotFunctions.R

PlotPiesR Documentation

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)
          

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.