data requirement for getLineages

[jimlin1668478052]

An error is reported when I try to use the function "getLineages":

spangler.sce <- getLineages(spangler.sce, cl)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘getLineages’ for signature ‘"SingleCellExperiment", "factor"’

spangler.sce is a SingleCellExperiment data converted from Seurat
cl is a list of factor (including numbers 0-9 in the form of characters)

The same problem occurs when I change cl into a vector:

spangler.sce <- getLineages(spangler.sce, c("0","1","2","3","4","5","6","7","8","9"))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘getLineages’ for signature ‘"SingleCellExperiment", "character"’

The function slingshot can work very well with the same SingleCellExperiment data:
spangler.sce <- slingshot(spangler.sce,clusterLabels = "seurat_clusters", reducedDim = "PCA")

[kstreet13]

Thanks for the report! I agree that this is strange behavior and I will add functionality to handle it in the next update.

Originally, I thought of slingshot() as being the main function and getLineages and getCurves as being low-level helpers that most people wouldn't interact with, so I didn't think it was necessary to add a method for this case. But it seems like a few people have had this issue, especially with larger datasets where getCurves can be slow.

[kstreet13]

Oh, sorry, I also should have mentioned that you can work around this by extracting the relevant parts of the SingleCellExperiment object and directly inputting them to getLineages. In your case, I think that would look like this:

getLineages(reducedDims(spangler.sce)$PCA, clusterLabels = cl)

Which will return a SlingshotDataSet object that can be used with getCurves.

[kstreet13]

Sorry for the delay. This is now implemented in the master branch here and in the devel branch of Bioconductor (slingshot version >= 1.3.1). Specifically, getLineages() and getCurves() now accept SingleCellExperiment objects as input. Thanks for the report!