AddAnnotation           AddAnnotation
AddBackground           AddBackground
AddFlowFrame            Add a flowFrame to the data variable of the
                        FlowSOM object
AddLabels               AddLabels
AddMST                  AddMST
AddNodes                AddNodes
AddPies                 AddPies
AddScale                AddScale
AddStars                AddStars
AddStarsPies            AddStarsPies
AggregateFlowFrames     Aggregate multiple FCS files together
AutoMaxNodeSize         AutoMaxNodeSize
BuildMST                BuildMST
BuildSOM                Build a self-organizing map
CountGroups             Calculate differences in cell counts between
                        groups
Dist.MST                Calculate distance matrix using a minimal
                        spanning tree neighborhood
FMeasure                F measure
FlowSOM                 Run the FlowSOM algorithm
FlowSOMSubset           FlowSOMSubset
FlowSOM_colors          FlowSOM default colors
FlowSOMmary             FlowSOMmary
GetCVs                  Get CV values for all clusters
GetChannels             GetChannels
GetClusterCVs           Get CV values for all clusters
GetClusterMFIs          Get MFI values for all clusters
GetClusterPercentagesPositive
                        Get percentage-positive values for all clusters
GetClusters             Get cluster label for all individual cells
GetCounts               GetCounts
GetFeatures             GetFeatures
GetFlowJoLabels         Process a FlowJo workspace file
GetMFIs                 Get MFI values for all clusters
GetMarkers              GetMarkers
GetMetaclusterCVs       GetMetaclusterCVs
GetMetaclusterMFIs      GetMetaclusterMFIs
GetMetaclusterPercentagesPositive
                        Get percentage-positive values for all
                        metaclusters
GetMetaclusters         Get metacluster label for all individual cells
GetPercentages          GetPercentages
GroupStats              GroupStats
Initialize_KWSP         Select k well spread points from X
Initialize_PCA          Create a grid from first 2 PCA components
ManualVector            Summarize the gating matrix into one vector,
                        only including the cell types of interest
MapDataToCodes          Assign nearest node to each datapoint
MetaClustering          MetaClustering
MetaclusterCVs          MetaclusterCVs
MetaclusterMFIs         MetaclusterMFIs
NClusters               NClusters
NMetaclusters           NMetaclusters
NewData                 NewData
ParseArcs               ParseArcs
ParseEdges              ParseEdges
ParseLayout             ParseLayout
ParseNodeSize           ParseNodeSize
ParseQuery              ParseQuery
ParseSD                 ParseSD Parses SD in FlowSOM object
Plot2DScatters          Plot2DScatters
PlotCenters             PlotCenters
PlotClusters2D          PlotClusters2D
PlotDimRed              PlotDimRed
PlotFileScatters        PlotFileScatters
PlotFlowSOM             PlotFlowSOM
PlotGroups              PlotGroups
PlotLabels              PlotLabels
PlotManualBars          PlotManualBars
PlotMarker              PlotMarker
PlotNode                PlotNode Plot star chart
PlotNumbers             PlotNumbers
PlotOutliers            PlotOutliers
PlotOverview2D          PlotOverview2D
PlotPies                PlotPies
PlotSD                  PlotSD
PlotStarLegend          PlotStarLegend
PlotStars               PlotStars
PlotVariable            PlotVariable
Purity                  Calculate mean weighted cluster purity
QueryMultiple           QueryMultiple
QueryStarPlot           QueryStarPlot
ReadInput               Read FCS-files or flowFrames
SOM                     Build a self-organizing map
SaveClustersToFCS       Write FlowSOM clustering results to the
                        original FCS files
ScaleStarHeights        ScaleStarHeights
TestOutliers            TestOutliers
UpdateFlowSOM           UpdateFlowSOM
UpdateMetaclusters      UpdateMetaclusters
UpdateNodeSize          UpdateNodeSize
get_channels            get_channels
get_markers             get_markers
gg_color_hue            gg_color_hue
metaClustering_consensus
                        MetaClustering
print.FlowSOM           Print FlowSOM object
query_multiple          query_multiple
