PlotSD: PlotSD

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

PlotSD

Description

Plot FlowSOM grid or tree, colored by standard deviation.

Usage

PlotSD(fsom, marker = NULL, ...)

Arguments

fsom	FlowSOM object, as generated by FlowSOM
marker	If a marker/channel is given, the sd for this marker is shown. Otherwise, the maximum ratio is used.
...	Additional arguments to pass to PlotFlowSOM

Value

Nothing is returned. A plot is drawn in which each node is colored depending on its standard deviation

See Also

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

Examples

# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata", "68983.fcs", package  = "FlowSOM")
flowSOM.res <- ReadInput(fileName, compensate  = TRUE, transform  = TRUE,
                         scale  = TRUE)
flowSOM.res <- BuildSOM(flowSOM.res, colsToUse  = c(9, 12, 14:18))
flowSOM.res <- BuildMST(flowSOM.res)

PlotSD(flowSOM.res)

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