PlotLabels {FlowSOM}R Documentation

Plot a label in each node

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)


[Package FlowSOM version 1.22.0 Index]