Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/quickPseudotime.R
A convenience wrapper to quickly compute a minimum spanning tree (MST) on the cluster centroids to obtain a pseudotime ordering of the cells. This function is now deprecated as it has been moved to the TSCAN package itself.
1 2 3 4 5 6 7 8  quickPseudotime(
x,
clusters,
use = 1,
outgroup = FALSE,
outscale = 3,
start = NULL
)

x 
A named list of numeric matrices containing dimensionality reduction results.
All matrices should have the same number of cells, i.e., rows.
Alternatively, a SingleCellExperiment containing such results in its 
clusters 
A factor of length equal to the number of cells in 
use 
Integer scalar or string specifying the entry of 
outgroup, outscale 
Arguments passed to 
start 
Arguments passed to 
This function simply calls, in order:
rowsum
, to compute the average lowdimensional coordinates for each cluster.
createClusterMST
on the average coordinates specified by use
.
orderClusterMST
on the average and percell coordinates specified by use
.
connectClusterMST
on the average coordinates for all entries of x
.
A List containing:
centered
, a list of numeric matrices containing the averaged coordinates for each cluster.
Each matrix corresponds to a dimensionality reduction result in x
.
mst
, a graph object containing the clusterlevel MST computed on the coordinates from use
.
ordering
, a numeric matrix of pseudotimes for various paths through the MST computed from use
.
connected
, a list of data.frames containing the edge coordinates between centers.
Each data.frame corresponds to a dimensionality reduction result in x
.
Aaron Lun
createClusterMST
and friends, for the functions that do the actual work.
1 2 3 4 5 6 7 8 9 10 11  # Mocking up some data:
library(scuttle)
sce < mockSCE(ncells=500)
sce < logNormCounts(sce)
sce < scater::runPCA(sce)
clusters < clusterSNNGraph(sce, use.dimred="PCA")
# Quickly computing the pseudotime:
out < quickPseudotime(sce, clusters, use="PCA")
out$mst
head(out$ordering)

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