plotTSCANClusterPseudo: Plot TSCAN pseudotime rooted from given cluster

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

Plot TSCAN pseudotime rooted from given cluster

Description

This function finds all paths that root from a given cluster useCluster. For each path, this function plots the recomputed pseudotime starting from the root on a scatter plot which contains cells only in this cluster. MST has to be pre-calculated with runTSCAN.

Usage

plotTSCANClusterPseudo(
  inSCE,
  useCluster,
  useReducedDim = "UMAP",
  combinePlot = c("all", "none")
)

Arguments

inSCE	Input SingleCellExperiment object.
useCluster	The cluster to be regarded as the root, has to existing in colData(inSCE)$TSCAN_clusters.
useReducedDim	Saved dimension reduction name in the SingleCellExperiment object. Required.
combinePlot	Must be either "all" or "none". "all" will combine plots of pseudotime along each path into a single .ggplot object, while "none" will output a list of plots. Default "all".

Value

combinePlot = "all"	A .ggplot object
combinePlot = "none"	A list of .ggplot

Author(s)

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
plotTSCANClusterPseudo(mouseBrainSubsetSCE, useCluster = 1,
                       useReducedDim = "TSNE_logcounts")

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