TrajectoryAnalysis {RCSL} | R Documentation

## Trajectory analysis

### Description

Trajectory analysis

### Usage

    TrajectoryAnalysis(
      gfData,
      drData,
      S,
      clustRes,
      fontSize = 12,
      TrueLabel,
      startPoint,
      dataName = "",
      sim = TRUE,
      simMeasure = "kendall",
      VisualMethod = "umap"
    )

### Arguments

`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

### Value

PseudoTimePlot, MSTPlot, TrajectoryPlot

### Examples

    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)

[Package RCSL version 1.2.0 Index]