PlotNumbers {FlowSOM} | R Documentation |
Plot cluster ids for each cluster
PlotNumbers(fsom, level = "clusters", maxNodeSize = 0, ...)
fsom |
FlowSOM object |
level |
Character string, should be either "clusters" or "metaclusters" |
maxNodeSize |
Determines the maximum nodesize. Default is 0.
See |
... |
Additional arguments to pass to |
Plot FlowSOM grid or tree, with in each node the cluster id.
Nothing is returned. A plot is drawn in which each node is labeled by its cluster id.
PlotStars
, PlotVariable
,
PlotFlowSOM
, PlotLabels
,
PlotMarker
, PlotPies
,
QueryStarPlot
, PlotSD
# Read from file, build self-organizing map and minimal spanning tree fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM") ff <- flowCore::read.FCS(fileName) ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]]) ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff, flowCore::colnames(ff)[8:18])) flowSOM.res <- FlowSOM(ff, scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10, seed = 1) # Plot the node IDs PlotNumbers(flowSOM.res) PlotNumbers(flowSOM.res, "metaclusters") PlotNumbers(flowSOM.res, view = "grid") PlotNumbers(flowSOM.res, maxNodeSize = 1, equalNodeSize = TRUE)