PlotCenters: PlotCenters

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

PlotCenters

Description

Plot cluster centers on a 2D plot

Usage

PlotCenters(fsom, marker1, marker2, MST = TRUE)

Arguments

fsom	FlowSOM object, as generated by BuildMST
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

Details

Plot FlowSOM nodes on a 2D scatter plot of the data

Value

Nothing is returned. A 2D scatter plot is drawn on which the nodes of the grid are indicated

See Also

PlotStars,PlotPies, PlotMarker,BuildMST

Examples

   # 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)
                  

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.