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


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Documentation for package ‘FlowSOM’ version 1.18.0

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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