A wrapper function which visualizes outputs from the
runTSCAN
function. Plots the pseudotime ordering of the cells
by projecting them onto the MST
plotTSCANResults(inSCE, useReducedDim)
Input SingleCellExperiment object.
Saved dimension reduction name in inSCE
object.
Required.
A plot with the pseudotime ordering of the cells by projecting them onto the MST.
data("scExample", package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
rowData(sce)$Symbol <- rowData(sce)$feature_name
rownames(sce) <- rowData(sce)$Symbol
sce <- scaterlogNormCounts(sce, assayName = "logcounts")
sce <- runDimReduce(inSCE = sce, method = "scaterPCA",
useAssay = "logcounts", reducedDimName = "PCA")
#> Thu Apr 28 11:27:26 2022 ... Computing Scater PCA.
sce <- runDimReduce(inSCE = sce, method = "rTSNE", useReducedDim = "PCA",
reducedDimName = "TSNE")
#> Thu Apr 28 11:27:26 2022 ... Computing RtSNE.
#> Warning: using `useReducedDim`, `run_pca` and `ntop` forced to be FALSE/NULL
sce <- runTSCAN (inSCE = sce, useReducedDim = "PCA", seed = NULL)
#> Thu Apr 28 11:27:27 2022 ... Running 'scran SNN clustering'
#> Cluster involved in path 4 are: 1:5
#> Number of estimated paths is 1
plotTSCANResults(inSCE = sce, useReducedDim = "TSNE")