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

## Documentation for package ‘FlowSOM’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- 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
GetClusters | Get cluster label for all individual cells
GetCVs | Get CV values for all clusters
GetFlowJoLabels | Process a flowjo workspace file
GetMetaclusters | Get metacluster label for all individual cells
GetMFIs | Get MFI values for all clusters
get_channels | get_channels
get_markers | get_markers
Initialize_KWSP | Select k well spread points from X
Initialize_PCA | Create a grid from first 2 PCA components
MapDataToCodes | Assign nearest node to each datapoint
MetaclusterCVs | MetaclusterCVs
MetaClustering | MetaClustering
metaClustering_consensus | MetaClustering
MetaclusterMFIs | MetaclusterMFIs
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
PlotLabels | Plot a label in each node
PlotMarker | Plot marker values
PlotNode | Plot star chart
PlotNumbers | Plot the index of each node
PlotOverview2D | Plot metaclusters on scatter plots
PlotPies | Plot comparison with other clustering
PlotSD | Plot SD
plotStarLegend | Plot legend for star plot
PlotStars | Plot star charts
PlotVariable | Plot a variable for all nodes
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
TestOutliers | Test if any cells are too far from their cluster centers
UpdateNodeSize | Update nodesize of FlowSOM object