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 |
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 |
PeaksAndValleys | Find peaks and valleys in one-dimensional data |
PlotCenters | Plot cluster centers on a 2D plot |
PlotClusters2D | Plot nodes on scatter plot |
PlotGroups | Plot differences between groups |
PlotMarker | Plot marker values |
PlotNumbers | Plot the index of each node |
PlotPies | Plot comparison with other clustering |
plotStarLegend | Plot legend for star plot |
PlotStars | Plot star charts |
PlotStarsSD | Plot standard deviation 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 |