plot3d error about slingshot HOT 3 CLOSED

Hi @lixin4306ren ,

Thanks for the report! It looks like this line of code is from the vignette and I was able to reproduce the error using the simulated dataset generated there (sim). However, since this is a SingleCellExperiment object, there is no plot3d method for it (I only defined a plot3d method for objects of the class SlingshotDataSet, since SingleCellExperiment objects are highly flexible and may contain multiple components worth plotting in 3D, beyond just the slingshot output). That said, an easy workaround would be something like this:

plot3d(SlingshotDataSet(sce))

But I should also note that in the vignette, I only used the top 2 PCs, so this line will still produce an error when using that dataset. If you adjust the earlier line where rd1 is defined to read

rd1 <- pca$x[,1:3]

then you will have the top 3 PCs and this should work as expected!

Best,
Kelly

from slingshot.

Hi Kelly,

slingshot_df <- data.frame(colData(deng_SCE)) Error in as.vector(x) : no method for coercing this S4 class to a vector

I have been trying to convert my slingshot object to a dataframe and not sure how to get out of this error. Could you look into this?

Thank you,
Aastha

from slingshot.

Sorry, how is this related to the original issue regarding 3D plotting? This seems like more of a general SingleCellExperiment question, but the colData should already be something analogous to a data frame, so I'm not sure why you would need to convert it.

from slingshot.