Plot MST pseudotime values on cell 2D embedding — plotTSCANResults • singleCellTK

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

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

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
#> Tue Jun 28 22:06:04 2022 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Tue Jun 28 22:06:05 2022 ...   Identified 2 clusters
#> Tue Jun 28 22:06:05 2022 ... Running TSCAN to estimate pseudotime
#> Tue Jun 28 22:06:05 2022 ...   Clusters involved in path index 2 are: 1, 2
#> Tue Jun 28 22:06:05 2022 ...   Number of estimated paths is 1
plotTSCANResults(inSCE = mouseBrainSubsetSCE,
                 useReducedDim = "TSNE_logcounts")
#> Scale for 'colour' is already present. Adding another scale for 'colour',
#> which will replace the existing scale.