FSPY-class              Class 'FSPY'
Rphenograph             RphenoGraph clustering
buildTree               buildTree
constraintMatrix        constraintMatrix
correctBatchFSPY        correctBatchFSPY
createFSPY              create an FSPY object
defLeafCells            definition of leaf cells
defRootCells            definition of root cells
fetchCell               Fetching cellls of FSPY
fetchClustMeta          Fetching clusters' metadata of FSPY
fetchPlotMeta           Fetching plot metadata of FSPY
find_neighbors          K Nearest Neighbour Search
flowSpy-package         Visualization and analyzation for flow
                        cytometry data
gatingMatrix            Apply gating on the matrix data
plot2D                  Visualization of 2D data of FSPY
plot3D                  Visualization of 3D data of FSPY
plotBranchHeatmap       Visualization heatmap of branch data of FSPY
plotCluster             Visualization of cluster data of FSPY
plotClusterHeatmap      Visualization heatmap of cluster data of FSPY
plotHeatmap             Visualization heatmap of data of FSPY
plotMarkerDensity       plotMarkerDensity
plotPieCluster          Visualization pie plot of cluster data of FSPY
plotPieTree             plot MST pie of FSPY
plotPseudotimeDensity   plot Pseudotime density of FSPY
plotPseudotimeTraj      plotPseudotimeTraj
plotTrajHeatmap         Visualization heatmap of intermediate cells of
                        FSPY
plotTree                plot MST of FSPY
plotViolin              Visualization violin plot of FSPY
processingCluster       processingCluster
runClara                runClara
runCluster              Specific Clustering Method Toolkits
runDiff                 Calculate differential expression markers
runDiffusionMap         Calculate diffusion map in FSPY
runExprsExtract         Extract the expression data from a FCS file
                        with preprocessing
runExprsMerge           Merge the expression matrix from multiple FCS
                        files with preprocessing
runFastPCA              Calculate principal components in FSPY
runHclust               runHclust
runKNN                  Calculate k-nearest neighbors of FSPY
runKmeans               runKmeans
runMclust               runMclust
runPhenograph           RphenoGraph clustering
runPseudotime           Calculation of Pseudotime
runSOM                  calculation SOM in FSPY object
runTSNE                 Calculate t-Distributed Stochastic Neighbor
                        Embedding in FSPY
runUMAP                 Calculating UMAP
runWalk                 Walk between root cells and leaf cells
subsetFSPY              subset FSPY object
updateClustMeta         Update clusters' meta information of FSPY
updatePlotMeta          Update plot meta information of FSPY
