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


[Up] [Top]

Documentation for package ‘FlowSOM’ version 2.16.0

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