PlotNode: Plot star chart

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

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	Colorpalette 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)
   
   # Plot stars indicating the MFI of the cells present in the nodes
   PlotNode(flowSOM.res$FlowSOM,1)

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