FlowSOM (version 1.4.0)

PlotClusters2D: Plot nodes on scatter plot

Description

Plot a 2D scatter plot. All cells of fsom$data are plotted in black, and those of the selected nodes are plotted in red. The nodes in the grid are indexed starting from the left bottom, first going right, then up. E.g. In a 10x10 grid, the node at top left will have index 91.

Usage

PlotClusters2D(fsom, marker1, marker2, nodes, main = "", col = "#FF0000", maxBgPoints = NULL, ...)

Arguments

fsom

FlowSOM object, as generated by BuildMST

marker1

Marker to plot on the x-axis

marker2

Marker to plot on the y-axis

nodes

Nodes of which the cells should be plotted in red

main

Title of the plot

col

Colors for all the cells in the selected nodes (ordered array)

maxBgPoints

Maximum number of background points to plot

...

Other parameters to pass on to plot

Value

Nothing is returned. A plot is drawn in which all cells are plotted in black and the cells of the selected nodes in red.

See Also

PlotNumbers,PlotCenters, BuildMST

Examples

   # Read from file, build self-organizing map and minimal spanning tree
   fileName <- system.file("extdata","lymphocytes.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 cells
   PlotClusters2D(flowSOM.res,1,2,91)