PlotLabels: Plot a label in each node

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

Description

Plot FlowSOM grid or tree, with in each node a label. Especially useful to show metacluster numbers

Usage

PlotLabels(
  fsom,
  labels,
  view = "MST",
  main = NULL,
  nodeSize = fsom$MST$size,
  fontSize = 1,
  backgroundValues = NULL,
  backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
  backgroundLim = NULL,
  backgroundBreaks = NULL
)

Arguments

fsom	FlowSOM object, as generated by BuildMST
labels	A label for every node
view	Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
main	Title of the plot
nodeSize	Nodesize. The plot might be easier to read if this is a constant number, e.g. 10 or 15
fontSize	Fontsize, passed to label.cex
backgroundValues	Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)
backgroundColor	Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors
backgroundLim	Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.
backgroundBreaks	Breaks to pass on to cut, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).

Value

Nothing is returned. A plot is drawn in which each node is assigned a label

See Also

PlotNumbers

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, ff@description$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
PlotLabels( flowSOM.res$FlowSOM, flowSOM.res$metaclustering, nodeSize=15)

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.