umap() produces matrix instead of S3 object

[umasstr]

I have a data frame, b, with 21 sample rows and 1789 uniquely-names gene rows.

> class(b)
[1] "data.frame"
> ncol(b)
[1] 1789
> nrow(b)
[1] 21

umap runs without error or warning. I think that umap is supposed to generate an S3 object, but I only get a 2-column matrix with coordinates. This is fine for generating the plot, but I wanted to extract other information from layout. Any suggestions? Thanks!

> um<-umap(b,n_neighbors = 10)
> class(um)
[1] "matrix"
> nrow(um)
[1] 21
> ncol(um)
[1] 2

[tkonopka]

Hi @umasstr. Yes, the output is supposed to be an S3 object. If you are getting a matrix, is it possible that you loaded package uwot after loading package umap? (Package uwot performs dimensional reduction in a similar way, but it has slightly different features and API.) If that's the case, and if you want to keep using both packages in the same R session, you can still run umap from this package by calling umap::umap(b).

[umasstr]

Wow, I wouldn't have thought of that. All set—runs quickly and without error or warning.
Thanks, and happy holidays!