PlotPseudoTime: Infer the pseudo-temporal ordering between the cell types...

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

Infer the pseudo-temporal ordering between the cell types using the distance from a cell type to the predefined starting cell type.

Description

Infer the pseudo-temporal ordering between the cell types using the distance from a cell type to the predefined starting cell type.

Usage

PlotPseudoTime(
  S,
  TrueLabel,
  startPoint,
  fontSize = 12,
  dataName = "",
  sim = TRUE
)

Arguments

S	the similarity matrix calculated by SimS() function
TrueLabel	the real cell types used to indicate the vertical axis
startPoint	the posiition of the starting cell in the matrix
fontSize	the font size of the plot
dataName	the name of the data that will be showed in the plot
sim	indicate the input data is simialrity matrix or not

Value

PstudoTime

PseudoTimePlot ggplot object of the pseudo-temporal ordering of cells

Examples

gfData <- GenesFilter(yan)
TrueLabel <- ann$cell_type1
res_SimS <- SimS(gfData)
PlotPseudoTime(res_SimS$S,TrueLabel,startPoint=1)

QinglinMei/RCSL documentation built on Feb. 16, 2024, 2:31 a.m.