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")
Input SingleCellExperiment object.
Saved dimension reduction name in inSCE
object.
Required.
A .ggplot
object with the pseudotime ordering of the cells
colored on a cell 2D embedding, and the MST path drawn on it.
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
useReducedDim = "PCA_logcounts")
#> Sat Mar 18 10:30:17 2023 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Sat Mar 18 10:30:17 2023 ... Identified 2 clusters
#> Sat Mar 18 10:30:17 2023 ... Running TSCAN to estimate pseudotime
#> Sat Mar 18 10:30:18 2023 ... Clusters involved in path index 2 are: 1, 2
#> Sat Mar 18 10:30:18 2023 ... 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.