plotTSCANResults: Plot MST pseudotime values on cell 2D embedding

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Plot MST pseudotime values on cell 2D embedding

Description

A wrapper function which visualizes outputs from the runTSCAN function. Plots the pseudotime ordering of the cells and project them onto the MST.

Usage

plotTSCANResults(inSCE, useReducedDim = "UMAP")

Arguments

inSCE	Input SingleCellExperiment object.
useReducedDim	Saved dimension reduction name in inSCE object. Required.

Value

A .ggplot object with the pseudotime ordering of the cells colored on a cell 2D embedding, and the MST path drawn on it.

Author(s)

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
plotTSCANResults(inSCE = mouseBrainSubsetSCE,
                 useReducedDim = "TSNE_logcounts")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.