PlotLabels {FlowSOM} | R Documentation |
Plot FlowSOM grid or tree, with in each node a label. Especially useful to show metacluster numbers
PlotLabels( fsom, labels, view = "MST", main = NULL, nodeSize = fsom$MST$size, fontSize = 1, backgroundValues = NULL, backgroundColor = function(n) { grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL, backgroundBreaks = NULL )
fsom |
FlowSOM object, as generated by |
labels |
A label for every node |
view |
Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST) |
main |
Title of the plot |
nodeSize |
Nodesize. The plot might be easier to read if this is a constant number, e.g. 10 or 15 |
fontSize |
Fontsize, passed to label.cex |
backgroundValues |
Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering) |
backgroundColor |
Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors |
backgroundLim |
Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues. |
backgroundBreaks |
Breaks to pass on to |
Nothing is returned. A plot is drawn in which each node is assigned a label
# 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, ff@description$SPILL) ff <- flowCore::transform(ff, flowCore::estimateLogicle(ff, flowCore::colnames(ff)[8:18])) flowSOM.res <- FlowSOM(ff, scale=TRUE, colsToUse=c(9,12,14:18), nClus = 10, seed = 1) # Plot the node IDs PlotLabels( flowSOM.res$FlowSOM, flowSOM.res$metaclustering, nodeSize=15)