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

In QinglinMei/RCSL: Rank Constrained Similarity Learning for single cell RNA sequencing data

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 Feb. 16, 2024, 2:31 a.m.