PlotNode: PlotNode Plot star chart

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

PlotNode Plot star chart

Description

Plot a star chart indicating median marker values of a single node

Usage

PlotNode(
  fsom,
  id,
  markers = fsom$map$colsUsed,
  colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan",
    "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")),
  main = paste0("Cluster ", id)
)

Arguments

fsom	FlowSOM object, as generated by BuildMST or the first element of the list returned by FlowSOM
id	Id of the node to plot (check PlotNumbers to get the ids)
markers	Array of markers to use. Default: the markers used to build the tree
colorPalette	Color palette to be used for the markers
main	Title of the plot

Value

Nothing is returned. A plot is drawn in which the node is represented by a star chart indicating the median fluorescence intensities.

See Also

PlotStars,PlotNumbers, FlowSOM

Examples

   # Read from file, build self-organizing map and minimal spanning tree
   fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
   flowSOM.res <- FlowSOM(fileName, compensate=TRUE,transform=TRUE,
                            scale=TRUE,colsToUse=c(9,12,14:18),nClus=10)
   
   # Deprecated, it is currently not possible anymore to plot an individual
   # node alone. If necessary, zooming in on a node can be approximated by
   # exagerating the size of the node.
   PlotStars(flowSOM.res, nodeSizes = c(100, rep(0,99)), maxNodeSize = 10)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.