PlotMarker: Plot marker values

Description Usage Arguments Value References See Also Examples

View source: R/3_buildMST.R

Description

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

Usage

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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

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

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

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