Error running plotSmoothers with one lineage sce object

[Jon-bioinfo]

I'm getting an error running plotSmoothers:
> plotSmoothers(sce, counts, gene = 'Fasn')
Error in pseudotime[lineageID == ii, ii] : incorrect number of dimensions

The counts, pca and clusters are from Seurat:
counts <- as.matrix(so@assays$RNA@counts)
lin <- getLineages(so@reductions$pca@cell.embeddings[, 1:10], clusterLabels = cl, start.clus = 4, end.clus=2)
crv <- getCurves(lin)
sce <- fitGAM(counts = counts[id, ], sds = crv, nknots = 7 )

I think this is due to having only one lineage and an sce object:

In the .plotSmoothers_sce function the code pseudotime <- slingshotColData[,grep(x = colnames(slingshotColData), pattern = "pseudotime")] returns a vector not a data frame when there is just one curve.

Thanks,

[HectorRDB]

Hey,
Thanks for pointing this out, this was indeed the issue. It should be fixed now, you can install the newest devel version of tradeSeq with

devtools::install_github("statOmics/tradeSeq")

Let me know if anything else is unclear. There should not be any other issues for the one lineage case but this situations has been less thoroughly benchmarked so there might be some more bugs.

[Jon-bioinfo]

Thanks,

The same problem exists in the .clusterExpressionPatterns function.

[HectorRDB]

Hi,
Thanks for being so thorough, it really help us a lot.