AddFlowFrame            Add a flowFrame to the data variable of the
                        FlowSOM object
AggregateFlowFrames     Aggregate multiple fcs files together
BuildMST                Build Minimal Spanning Tree
BuildSOM                Build a self-organizing map
CountGroups             Calculate differences in cell counts between
                        groups
Dist.MST                Calculate distance matrix using a minimal
                        spanning tree neighbourhood
FMeasure                F measure
FlowSOM                 Run the FlowSOM algorithm
FlowSOMSubset           FlowSOM subset
Initialize              Select k well spread points from X
MapDataToCodes          Assign nearest node to each datapoint
MetaClustering          MetaClustering
NewData                 Map new data to a FlowSOM grid
PlotCenters             Plot cluster centers on a 2D plot
PlotClusters2D          Plot nodes on scatter plot
PlotGroups              Plot differences between groups
PlotMarker              Plot marker values
PlotNode                Plot star chart
PlotNumbers             Plot the index of each node
PlotPies                Plot comparison with other clustering
PlotStars               Plot star charts
PlotVariable            Plot a variable for all nodes
ProcessGatingML         Process a gatingML file
Purity                  Calculate mean weighted cluster purity
QueryStarPlot           Query a certain cell type
ReadInput               Read fcs-files or flowframes
SOM                     Build a self-organizing map
SaveClustersToFCS       Write FlowSOM clustering results to the
                        original FCS files
UpdateNodeSize          Update nodesize of FlowSOM object
computeBackgroundColor
                        Internal function for computing background
                        nodes
metaClustering_consensus
                        MetaClustering
plotStarLegend          Plot legend for star plot
