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

## Documentation for package ‘FlowSOM’ version 1.8.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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