data requirement for getLineages about slingshot HOT 3 CLOSED

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.

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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.

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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!

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