PlotStars: Plot star charts

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

Description

Plot FlowSOM grid or tree, where each node is represented by a star chart indicating median marker values

Usage

PlotStars(
  fsom,
  markers = fsom$map$colsUsed,
  view = "MST",
  colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan",
    "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
  starBg = "white",
  backgroundValues = NULL,
  backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) },
  backgroundLim = NULL,
  backgroundBreaks = NULL,
  backgroundSize = NULL,
  thresholds = NULL,
  legend = TRUE,
  query = NULL,
  range = "all",
  main = ""
)

Arguments

fsom	FlowSOM object, as generated by BuildMST
markers	Array of markers to use. Default: the markers used to build the tree
view	Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)
colorPalette	Colorpalette to be used for the markers
starBg	Background color inside the star circle. Default is "white". Can also be put to "transparent" (as was the case for older versions).
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).
backgroundSize	Size of the background circles. Default 15.
thresholds	Optional. Array containing a number for each of the markers to be used as the split between high/low. If provided, the percentage of positive cells is indicated instead of the MFI
legend	Logical, if TRUE add a legend
query	Show a low/high profile for certain markers in the legend. See also QueryStarPlot
range	If "all" (default), range is computed on all markers passed, if "one", range is computed on every marker separately. The height of the pie pieces will be computed relative to this range.
main	Title of the plot

Value

Nothing is returned. A plot is drawn in which each node is represented by a star chart indicating the median fluorescence intensities. Resets the layout back to 1 plot at the end.

See Also

PlotPies,PlotMarker, 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 stars indicating the MFI of the cells present in the nodes
   PlotStars(flowSOM.res)

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