TrajectoryAnalysis {RCSL} | R Documentation |
Trajectory analysis
TrajectoryAnalysis( gfData, drData, S, clustRes, fontSize = 12, TrueLabel, startPoint, dataName = "", sim = TRUE, simMeasure = "kendall", VisualMethod = "umap" )
gfData |
preprocessed gene expression data (each column represent a cell) |
drData |
preprocessed gene expression data (each column represent a cell) |
S |
the similarity matrix calculated by SimS() function |
clustRes |
the clustering results identified by RCSL |
fontSize |
the size of font in the plot |
TrueLabel |
the real cell types used to indicate the vertical axis |
startPoint |
the posiition of the starting cell in the matrix |
dataName |
the name of the data that will be showed in the plot |
sim |
indicate the input data is simialrity matrix or not |
simMeasure |
the calculation method of measuring the cluster centers' similarity |
VisualMethod |
the display method of 2-D visualization |
PseudoTimePlot, MSTPlot, TrajectoryPlot
gfData <- GenesFilter(yan) TrueLabel <- ann$cell_type1 res_SimS <- SimS(gfData) C <- EstClusters(res_SimS$drData,res_SimS$S) res_BDSM <- BDSM(res_SimS$S,C) TrajectoryAnalysis(gfData,res_SimS$drData,res_SimS$S,res_BDSM$y, TrueLabel=TrueLabel,startPoint=1)