search

kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
259 stars 42 forks source link

Unable to plot lines #217

Closed SebastianMHJohn closed 1 year ago

SebastianMHJohn commented 1 year ago

Hello Slingshot-team, thanks for the great package, but I'm having problems when trying to plot lines onto my UMAP-plot. When running the function: lines() I'm getting the error:

Error in as.vector(x, mode = "numeric") : no method for coercing this S4 class to a vector

My object is a SlingshotDataSet object:

image

For the previous workflow, I tried the wrapper-function slingshot() as used in (https://bustools.github.io/BUS_notebooks_R/slingshot.html) and also the separated approach as in (https://nbisweden.github.io/workshop-archive/workshop-scRNAseq/2020-01-27/labs/compiled/slingshot/slingshot.html#basic_processing_with_seurat_pipeline).

I would be grateful for any suggestion or tip, thanks in advance, Best wishes.

kstreet13 commented 1 year ago

Hi @SebastianMHJohn,

Thanks for reaching out! I think the issue is that your object is actually a PseudotimeOrdering object, which doesn't have an associated lines method. If you call lines(SlingshotDataSet(<object>)), you should get the result you're looking for.

Also, I generally encourage people to use the official slingshot package vignette: https://bioconductor.org/packages/release/bioc/vignettes/slingshot/inst/doc/vignette.html This is mostly because I can't guarantee that third-party workflows like the one you mentioned will remain up-to-date.

Best, Kelly

SebastianMHJohn commented 1 year ago

Thanks for your response, it worked