PlotVariable: Plot a variable for all nodes

Description Usage Arguments Value See Also Examples

View source: R/3_buildMST.R

Description

Plot FlowSOM grid or tree, coloured by node values given in variable

Usage

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PlotVariable(fsom, variable, view = "MST", main = NULL,
  colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF",
  "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
  symmetric = FALSE, lim = NULL, backgroundValues = NULL,
  backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
  backgroundLim = NULL, backgroundBreaks = NULL)

Arguments

fsom

FlowSOM object, as generated by BuildMST

variable

Vector containing a value for each node

view

Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)

main

Title of the plot

colorPalette

Color palette to use

symmetric

Plot colours symmetric around zero

lim

Variable limits

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 coloured depending on its value for the given variable

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 some random values
rand <- runif(flowSOM.res$map$nNodes)
PlotVariable(flowSOM.res,rand)

FlowSOM documentation built on May 20, 2017, 9:36 p.m.

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