Wrapper for obtaining a pseudotime ordering of the cells by projecting them onto the minimum spanning tree (MST)
runTSCAN(inSCE, useReducedDim = "PCA", cluster = NULL, seed = 12345)
Input SingleCellExperiment object.
Character. A low-dimension representation in
reducedDims
, will be used for both clustering if cluster
not
specified and MST construction. Default "PCA"
.
Grouping for each cell in inSCE
. A vector with equal
length to the number of the cells in inSCE
, or a single character for
retriving colData
variable. Default NULL
, will run
runScranSNN
to obtain.
An integer. Random seed for clustering if cluster
is not
specified. Default 12345
.
The input inSCE
object with pseudotime ordering of the cells
along the paths and the cluster label stored in colData
, and other
unstructured information in metadata
.
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
useReducedDim = "PCA_logcounts")
#> Sat Mar 18 10:31:31 2023 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Sat Mar 18 10:31:32 2023 ... Identified 2 clusters
#> Sat Mar 18 10:31:32 2023 ... Running TSCAN to estimate pseudotime
#> Sat Mar 18 10:31:32 2023 ... Clusters involved in path index 2 are: 1, 2
#> Sat Mar 18 10:31:32 2023 ... Number of estimated paths is 1