PlotMST: Plot the visualization of constructed Minimum Spanning Tree...

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

Plot the visualization of constructed Minimum Spanning Tree based on the clustering results of RCSL

Description

Plot the visualization of constructed Minimum Spanning Tree based on the clustering results of RCSL

Usage

PlotMST(
  drData,
  clustRes,
  TrueLabel,
  dataName = "",
  fontSize = 12,
  VisualMethod = "umap"
)

Arguments

drData	preprocessed gene expression data
clustRes	the clustering results identified by RCSL
TrueLabel	the real cell types to color the dots in plot
dataName	the name of the data that will be showed in the plot
fontSize	the font size of the plot
VisualMethod	the method for 2D visualization including UMAP,t-SNE and PCA

Value

MSTPlot ggplot object of the visualization of constructed MST

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)
PlotMST(res_SimS$drData,res_BDSM$y,TrueLabel)

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