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

## Documentation for package ‘FlowSOM’ version 2.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
FlowSOM | Run the FlowSOM algorithm
FlowSOMmary | FlowSOMmary
FlowSOMSubset | FlowSOMSubset
FlowSOM_colors | FlowSOM default colors
FMeasure | F measure
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
GetCVs | Get CV values for all clusters
GetFeatures | GetFeatures
GetFlowJoLabels | Process a FlowJo workspace file
GetMarkers | GetMarkers
GetMetaclusterCVs | GetMetaclusterCVs
GetMetaclusterMFIs | GetMetaclusterMFIs
GetMetaclusterPercentagesPositive | Get percentage-positive values for all metaclusters
GetMetaclusters | Get metacluster label for all individual cells
GetMFIs | Get MFI values for all clusters
GetPercentages | GetPercentages
get_channels | get_channels
get_markers | get_markers
gg_color_hue | gg_color_hue
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
MetaclusterCVs | MetaclusterCVs
MetaClustering | MetaClustering
metaClustering_consensus | MetaClustering
MetaclusterMFIs | MetaclusterMFIs
NClusters | NClusters
NewData | NewData
NMetaclusters | NMetaclusters
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
print.FlowSOM | Print FlowSOM object
Purity | Calculate mean weighted cluster purity
QueryMultiple | QueryMultiple
QueryStarPlot | QueryStarPlot
query_multiple | query_multiple
ReadInput | Read FCS-files or flowFrames
SaveClustersToFCS | Write FlowSOM clustering results to the original FCS files
ScaleStarHeights | ScaleStarHeights
SOM | Build a self-organizing map
TestOutliers | TestOutliers
UpdateFlowSOM | UpdateFlowSOM
UpdateMetaclusters | UpdateMetaclusters
UpdateNodeSize | UpdateNodeSize