Man pages for FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
| 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... |
| FlowSOM | Run the FlowSOM algorithm |
| FlowSOMSubset | FlowSOM subset |
| FMeasure | F measure |
| get_channels | get_channels |
| GetClusters | Get cluster label for all individual cells |
| GetCVs | Get CV values for all clusters |
| GetFlowJoLabels | Process a flowjo workspace file |
| get_markers | get_markers |
| GetMetaclusters | Get metacluster label for all individual cells |
| GetMFIs | Get MFI values for all clusters |
| 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 |
