Using self-organizing maps for visualization and interpretation
of cytometry data
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Documentation for package ‘FlowSOM’ version 2.6.0
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 |
| 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 |