Using self-organizing maps for visualization and interpretation of cytometry data

Documentation for package ‘FlowSOM’ version 1.8.0

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
computeBackgroundColor	Internal function for computing background nodes
CountGroups	Calculate differences in cell counts between groups
Dist.MST	Calculate distance matrix using a minimal spanning tree neighbourhood
FlowSOM	Run the FlowSOM algorithm
FlowSOMSubset	FlowSOM subset
FMeasure	F measure
Initialize	Select k well spread points from X
MapDataToCodes	Assign nearest node to each datapoint
MetaClustering	MetaClustering
metaClustering_consensus	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
plotStarLegend	Plot legend for star plot
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
SaveClustersToFCS	Write FlowSOM clustering results to the original FCS files
SOM	Build a self-organizing map
UpdateNodeSize	Update nodesize of FlowSOM object