# A Toolkit for Flow And Mass Cytometry Data

## Documentation for package ‘CytoTree’ version 1.4.0

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

## Help Pages

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