PlotOverview2D: Plot metaclusters on scatter plots

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

Description

Write multiple 2D scatter plots to a png file. All cells of fsom$data are plotted in black, and those of the selected metaclusters are plotted in color.

Usage

PlotOverview2D(fsom, markerlist, metaclusters, colors = NULL, ff, ...)

Arguments

fsom	FlowSOM object, as generated by FlowSOM. If using a FlowSOM object as generated by BuildMST, it needs to be wrapped in a list, list(FlowSOM = fsom, metaclustering = metaclustering).
markerlist	List in which each element is a pair of marker names
metaclusters	Metaclusters of interest
colors	Named vector with color value for each metacluster. If NULL (default) colorbrewer "paired" is interpolated
ff	flowFrame to use as reference for the marker names
...	Other parameters to pass on to PlotClusters2D

Value

Nothing is returned, but a plot is drawn for every markerpair and every metacluster. The individual cells are colored, and the center of each FlowSOM cluster is indicated with a blue cross.

See Also

PlotClusters2D

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,
                          seed = 1)
                          
   # Plot cells
   markers_of_interest = list(c("FSC-A", "SSC-A"),
                              c("CD3", "CD19"),
                              c("TCRb", "TCRyd"),
                              c("CD4", "CD8"))
   metaclusters_of_interest = 1:10
   
   # Recommended to write to png
   
   png("Markeroverview.png",
       width = 500 * length(markers_of_interest),
       height = 500 * length(metaclusters_of_interest))
   PlotOverview2D(flowSOM.res,
                  markerlist = markers_of_interest,
                  metaclusters = metaclusters_of_interest,
                  pchCluster = 19,
                  ff = flowCore::read.FCS(fileName))
   dev.off()

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