| 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)