PlotSD: Plot SD

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

Description

— Function in development, use with caution — Plot FlowSOM grid or tree, coloured by standard deviaton

Usage

PlotSD(
  fsom,
  marker = NULL,
  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
marker	If a marker is given, the sd for this marker is shown. Otherwise, the maximum ratio is used.
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).

Details

From suggestion in email: I am currently considering a way to summarize for each node all the SD as one value. After computing the SD matrix (nrow = # nodes, ncol = # markers), I compute the median value per column, then divide the SD matrix by it, and finally take the maximum ratio of each line (aka node). Doing so I got a unique dispersion score per node.

Value

Nothing is returned. A plot is drawn in which each node is coloured depending on its standard deviation

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)

PlotSD(flowSOM.res)

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