Plot TSCAN pseudotime rooted from given cluster

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.

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

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
#> Tue Jun 28 22:05:56 2022 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Tue Jun 28 22:05:57 2022 ...   Identified 2 clusters
#> Tue Jun 28 22:05:57 2022 ... Running TSCAN to estimate pseudotime
#> Tue Jun 28 22:05:57 2022 ...   Clusters involved in path index 2 are: 1, 2
#> Tue Jun 28 22:05:57 2022 ...   Number of estimated paths is 1
plotTSCANClusterPseudo(mouseBrainSubsetSCE, useCluster = 1,
                       useReducedDim = "TSNE_logcounts")
#> Warning: Removed 1 rows containing missing values (geom_text_repel).