PlotNumbers: Plot the index of each node

Description Usage Arguments Value See Also Examples

View source: R/3_buildMST.R

Description

Plot FlowSOM grid or tree, with in each node a number indicating it's index

Usage

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

Arguments

fsom

FlowSOM object, as generated by BuildMST

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

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 number

See Also

PlotMarker,PlotStars, PlotPies,PlotCenters, BuildMST

Examples

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# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata","lymphocytes.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)

# Plot the node IDs
PlotNumbers(flowSOM.res)

# Adapt node size for easier readability
PlotNumbers(flowSOM.res, nodeSize=14)

FlowSOM documentation built on Nov. 17, 2017, 10:04 a.m.