PlotMarker: Plot marker values

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

Description

Plot FlowSOM grid or tree, coloured by node values for a specific marker

Usage

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

Arguments

fsom	FlowSOM object, as generated by BuildMST
marker	Name or index of marker to plot
view	Preferred view, options: "MST" (default), "grid" or "tSNE" (if this option was selected while building the MST)
main	Title of the plot
colorPalette	Color palette to use
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
backgroundBreaks	Breaks to pass on to cut, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).
backgroundLim	Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.

Value

Nothing is returned. A plot is drawn in which each node is coloured depending on its median value for the given marker

References

This visualization technique resembles SPADE results. M. Linderman, P. Qiu, E. Simonds and Z. Bjornson (). spade: SPADE – An analysis and visualization tool for Flow Cytometry. R package version 1.12.2. http://cytospade.org

See Also

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 one marker
PlotMarker(flowSOM.res,"FSC-A")

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