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")
)
Input SingleCellExperiment object.
The cluster to be regarded as the root, has to existing in
colData(inSCE)$TSCAN_clusters
.
Saved dimension reduction name in the SingleCellExperiment object. Required.
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"
.
A .ggplot
object
A list of .ggplot
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
useReducedDim = "PCA_logcounts")
#> Sat Mar 18 10:30:10 2023 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Sat Mar 18 10:30:10 2023 ... Identified 2 clusters
#> Sat Mar 18 10:30:10 2023 ... Running TSCAN to estimate pseudotime
#> Sat Mar 18 10:30:10 2023 ... Clusters involved in path index 2 are: 1, 2
#> Sat Mar 18 10:30:10 2023 ... Number of estimated paths is 1
plotTSCANClusterPseudo(mouseBrainSubsetSCE, useCluster = 1,
useReducedDim = "TSNE_logcounts")
#> Warning: Removed 1 rows containing missing values (`geom_text_repel()`).