TrajectoryAnalysis: Trajectory analysis

TrajectoryAnalysisR 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)


QinglinMei/RCSL documentation built on April 6, 2022, 9:13 p.m.