Man pages for CytoTree
A Toolkit for Flow And Mass Cytometry Data

addMetaDataAdd meta information of CYT
changeMarkerChange marker used in the calculation of CYT
createCYTcreate a CYT object
CYT-classClass 'CYT'
CytoTree-packageVisualization and analyzation for flow cytometry data
defLeafCellsdefinition of leaf cells
defRootCellsdefinition of root cells
fetchCellFetching cellls of CYT
fetchClustMetaFetching clusters' metadata of CYT
fetchPlotMetaFetching plot metadata of CYT
find_neighborsK Nearest Neighbour Search
gatingMatrixApply gating on the matrix data
plot2DVisualization of 2D data of CYT
plot3DVisualization of 3D data of CYT
plotBranchHeatmapVisualization heatmap of branch data of CYT
plotClusterVisualization of cluster data of CYT
plotClusterHeatmapVisualization heatmap of cluster data of CYT
plotHeatmapVisualization heatmap of data of CYT
plotPieClusterVisualization pie plot of cluster data of CYT
plotPieTreeplot MST pie of CYT
plotPseudotimeDensityplot Pseudotime density of CYT
plotTrajHeatmapVisualization heatmap of intermediate cells of CYT
plotTreeplot MST of CYT
plotViolinVisualization violin plot of CYT
RphenographRphenoGraph clustering
runClusterSpecific Clustering Method Toolkits
runDiffCalculate differential expression markers
runDiffusionMapCalculate diffusion map in CYT
runExprsExtractExtract the expression data from a FCS file with...
runExprsMergeMerge the expression matrix from multiple FCS files with...
runFastPCACalculate principal components in CYT
runKNNCalculate k-nearest neighbors of CYT
runPhenographRphenoGraph clustering
runPseudotimeCalculation of Pseudotime
runSOMcalculation SOM in CYT object
runTSNECalculate t-Distributed Stochastic Neighbor Embedding in CYT
runUMAPCalculating UMAP
runWalkWalk between root cells and leaf cells
show-CYT-methodCYT show method
subsetCYTsubset CYT object
updateClustMetaUpdate clusters' meta information of CYT
updatePlotMetaUpdate plot meta information of CYT
CytoTree documentation built on Nov. 10, 2020, 2 a.m.