PlotCenters {FlowSOM} | R Documentation |
Plot cluster centers on a 2D plot
PlotCenters(fsom, marker1, marker2, MST = TRUE)
fsom |
FlowSOM object, as generated by |
marker1 |
Marker to show on the x-axis |
marker2 |
Marker to show on the y-axis |
MST |
Type of visualization, if 1 plot tree, else plot grid |
Plot FlowSOM nodes on a 2D scatter plot of the data
Nothing is returned. A 2D scatter plot is drawn on which the nodes of the grid are indicated
PlotStars
,PlotPies
,
PlotMarker
,BuildMST
# Read from file, build self-organizing map and minimal spanning tree fileName <- system.file("extdata", "68983.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 centers plot <- Plot2DScatters(flowSOM.res, channelpairs = list(c("FSC-A","SSC-A")), clusters = list(seq_len(NClusters(flowSOM.res))), maxPoints = 0, plotFile = NULL)