PlotNode: PlotNode Plot star chart

View source: R/6_deprecated.R

PlotNodeR Documentation

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)


SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.