# A Toolkit for Flow And Mass Cytometry Data

## Documentation for package ‘flowSpy’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

flowSpy-package | Visualization and analyzation for flow cytometry data
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 | Visualization and analyzation for flow cytometry data
FSPY | Class 'FSPY'
FSPY-class | Class 'FSPY'
FSPY-class, | Class 'FSPY'
FSPYclass, | Class 'FSPY'
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
Rphenograph | RphenoGraph clustering
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
runKmeans | runKmeans
runKNN | Calculate k-nearest neighbors of FSPY
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