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

AddFlowFrameAdd a flowFrame to the data variable of the FlowSOM object
AggregateFlowFramesAggregate multiple fcs files together
BuildMSTBuild Minimal Spanning Tree
BuildSOMBuild a self-organizing map
computeBackgroundColorInternal function for computing background nodes
CountGroupsCalculate differences in cell counts between groups
Dist.MSTCalculate distance matrix using a minimal spanning tree...
FlowSOMRun the FlowSOM algorithm
FlowSOMSubsetFlowSOM subset
FMeasureF measure
GetClustersGet cluster label for all individual cells
GetCVsGet CV values for all clusters
GetFlowJoLabelsProcess a flowjo workspace file
GetMetaclustersGet metacluster label for all individual cells
GetMFIsGet MFI values for all clusters
Initialize_KWSPSelect k well spread points from X
Initialize_PCACreate a grid from first 2 PCA components
MapDataToCodesAssign nearest node to each datapoint
NewDataMap new data to a FlowSOM grid
PlotCentersPlot cluster centers on a 2D plot
PlotClusters2DPlot nodes on scatter plot
PlotGroupsPlot differences between groups
PlotLabelsPlot a label in each node
PlotMarkerPlot marker values
PlotNodePlot star chart
PlotNumbersPlot the index of each node
PlotOverview2DPlot metaclusters on scatter plots
PlotPiesPlot comparison with other clustering
PlotSDPlot SD
plotStarLegendPlot legend for star plot
PlotStarsPlot star charts
PlotVariablePlot a variable for all nodes
PurityCalculate mean weighted cluster purity
QueryStarPlotQuery a certain cell type
ReadInputRead fcs-files or flowframes
SaveClustersToFCSWrite FlowSOM clustering results to the original FCS files
SOMBuild a self-organizing map
TestOutliersTest if any cells are too far from their cluster centers
UpdateNodeSizeUpdate nodesize of FlowSOM object
FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.