PlotTrajectory: Infer the developmental trajectories based on the clustering...

PlotTrajectoryR Documentation

Infer the developmental trajectories based on the clustering results from RCSL

Description

Infer the developmental trajectories based on the clustering results from RCSL

Usage

PlotTrajectory(
  gfData,
  clustRes,
  TrueLabel,
  lineage,
  fontSize = 12,
  dataName = "",
  VisualMethod = "umap"
)

Arguments

gfData

preprocessed gene expression data (each column represent a cell)

clustRes

the clustering results identified by RCSL

TrueLabel

the real cell types

lineage

the lineage obtained by getLineage()

fontSize

the size of font in the plot

dataName

the name of the data that will be showed in the plot

VisualMethod

the display method of 2-D visualization

Value

TrajectoryPlot ggplot object of the inferred developmental trajectories

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)
Pseudo <- PlotPseudoTime(res_SimS$S,TrueLabel,startPoint=1)
Linea <- getLineage(res_SimS$drData,res_BDSM$y,Pseudo$pseudoTime)
PlotTrajectory(gfData,res_BDSM$y,TrueLabel,lineage=Linea)


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