PlotNode {FlowSOM} | R Documentation |
Plot a star chart indicating median marker values of a single node
PlotNode( fsom, id, markers = fsom$map$colsUsed, colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), main = paste0("Cluster ", id) )
fsom |
FlowSOM object, as generated by |
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 |
Colorpalette to be used for the markers |
main |
Title of the plot |
Nothing is returned. A plot is drawn in which the node is represented by a star chart indicating the median fluorescence intensities.
PlotStars
,PlotNumbers
,
FlowSOM
# 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)