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

AddAnnotationAddAnnotation
AddBackgroundAddBackground
AddFlowFrameAdd a flowFrame to the data variable of the FlowSOM object
AddLabelsAddLabels
AddMSTAddMST
AddNodesAddNodes
AddPiesAddPies
AddScaleAddScale
AddStarsAddStars
AddStarsPiesAddStarsPies
AggregateFlowFramesAggregate multiple FCS files together
AutoMaxNodeSizeAutoMaxNodeSize
BuildMSTBuildMST
BuildSOMBuild a self-organizing map
CountGroupsCalculate differences in cell counts between groups
Dist.MSTCalculate distance matrix using a minimal spanning tree...
FlowSOMRun the FlowSOM algorithm
FlowSOM_colorsFlowSOM default colors
FlowSOMmaryFlowSOMmary
FlowSOMSubsetFlowSOMSubset
FMeasureF measure
get_channelsget_channels
GetChannelsGetChannels
GetClusterCVsGet CV values for all clusters
GetClusterMFIsGet MFI values for all clusters
GetClusterPercentagesPositiveGet percentage-positive values for all clusters
GetClustersGet cluster label for all individual cells
GetCountsGetCounts
GetCVsGet CV values for all clusters
GetFeaturesGetFeatures
GetFlowJoLabelsProcess a FlowJo workspace file
GetMajorityLabelsGetMajorityLabels
get_markersget_markers
GetMarkersGetMarkers
GetMetaclusterCVsGetMetaclusterCVs
GetMetaclusterMFIsGetMetaclusterMFIs
GetMetaclusterPercentagesPositiveGet percentage-positive values for all metaclusters
GetMetaclustersGet metacluster label for all individual cells
GetMFIsGet MFI values for all clusters
GetPercentagesGetPercentages
gg_color_huegg_color_hue
GroupStatsGroupStats
Initialize_KWSPSelect k well spread points from X
Initialize_PCACreate a grid from first 2 PCA components
ManualVectorSummarize the gating matrix into one vector, only including...
MapDataToCodesAssign nearest node to each datapoint
MetaclusterCVsMetaclusterCVs
MetaClusteringMetaClustering
metaClustering_consensusMetaClustering
MetaclusterMFIsMetaclusterMFIs
NClustersNClusters
NewDataNewData
NMetaclustersNMetaclusters
ParseArcsParseArcs
ParseEdgesParseEdges
ParseLayoutParseLayout
ParseNodeSizeParseNodeSize
ParseQueryParseQuery
ParseSDParseSD Parses SD in FlowSOM object
pipePipe operator
Plot1DScattersPlot1DScatters
Plot2DScattersPlot2DScatters
PlotCentersPlotCenters
PlotClusters2DPlotClusters2D
PlotDimRedPlotDimRed
PlotFileScattersPlotFileScatters
PlotFlowSOMPlotFlowSOM
PlotGroupsPlotGroups
PlotLabelsPlotLabels
PlotManualBarsPlotManualBars
PlotMarkerPlotMarker
PlotNodePlotNode Plot star chart
PlotNumbersPlotNumbers
PlotOutliersPlotOutliers
PlotOverview2DPlotOverview2D
PlotPiesPlotPies
PlotSDPlotSD
PlotStarLegendPlotStarLegend
PlotStarsPlotStars
PlotVariablePlotVariable
print.FlowSOMPrint FlowSOM object
PurityCalculate mean weighted cluster purity
query_multiplequery_multiple
QueryMultipleQueryMultiple
QueryStarPlotQueryStarPlot
ReadInputRead FCS-files or flowFrames
SaveClustersToFCSWrite FlowSOM clustering results to the original FCS files
ScaleStarHeightsScaleStarHeights
SOMBuild a self-organizing map
TestOutliersTestOutliers
UpdateFlowSOMUpdateFlowSOM
UpdateMetaclustersUpdateMetaclusters
UpdateNodeSizeUpdateNodeSize
saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.