PlotNumbers: PlotNumbers

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

PlotNumbers

Description

Plot cluster ids for each cluster

Usage

PlotNumbers(fsom, level = "clusters", maxNodeSize = 0, ...)

Arguments

fsom	FlowSOM object
level	Character string, should be either "clusters" or "metaclusters". Can be abbreviated.
maxNodeSize	Determines the maximum node size. Default is 0. See PlotFlowSOM for more options.
...	Additional arguments to pass to PlotLabels and to PlotFlowSOM

Details

Plot FlowSOM grid or tree, with in each node the cluster id.

Value

Nothing is returned. A plot is drawn in which each node is labeled by its cluster id.

See Also

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

Examples

# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
ff <- flowCore::read.FCS(fileName)
ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]])
ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff,
                                               flowCore::colnames(ff)[8:18]))
flowSOM.res <- FlowSOM(ff,
                       scale = TRUE,
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10,
                       seed = 1)

# Plot the node IDs
PlotNumbers(flowSOM.res)
PlotNumbers(flowSOM.res, "metaclusters")

PlotNumbers(flowSOM.res,
            view = "grid")

PlotNumbers(flowSOM.res,
            maxNodeSize = 1,
            equalNodeSize = TRUE)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.