PlotVariable: Plot a variable for all nodes

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

Description

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

Usage

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

# 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)

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

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