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


[Up] [Top]

Documentation for package ‘FlowSOM’ version 1.6.0

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
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