Refactor from/to Seurat conversion #183
Conversation
rcannood
commented
Sep 19, 2024
•
rcannood
commented
- Redesigned the from_Seurat / to_Seurat conversion functions
|
Note: Could use https://satijalab.github.io/seurat-object/reference/UpdateSeuratObject.html to update a Seurat <v5 object to v5 in |
rcannood
changed the title
R/check_requires.R
Outdated
| "To continue, install {cli::qty(missing)}{?it/them} using", | ||
| "{.code install.packages(c({missing_str}))}" |
There was a problem hiding this comment.
These instructions won't work for Bioconductor packages. Fixing that should probably be a separate issue. And/or maybe one about updating all messages/warning/errors to use {cli} if we are going to depend on it anyway?
There was a problem hiding this comment.
These instructions won't work for Bioconductor packages.
Fixed!
updating all messages/warning/errors to use {cli} if we are going to depend on it anyway?
I'd like that, but let's do this in a separate PR 😅
R/Seurat.R
Outdated
| seurat_obj[[key]] <- SeuratObject::CreateAssayObject(counts = layer_) | ||
| # trackstatus: class=Seurat, feature=get_uns, status=done | ||
| # trackstatus: class=Seurat, feature=get_varp, status=done | ||
| obj@misc <- list() |
This comment was marked as resolved.
This comment was marked as resolved.
Sorry, something went wrong.
Co-authored-by: Luke Zappia <[email protected]>
|
Phew. I think I addressed most of the comments, except:
Also,
|
| #' @examples | ||
| #' ad <- AnnData( | ||
| #' X = matrix(1:5, 3L, 5L), | ||
| #' obs = data.frame(row.names = LETTERS[1:3], cell = 1:3), | ||
| #' var = data.frame(row.names = letters[1:5], gene = 1:5) | ||
| #' ) | ||
| #' to_Seurat(ad) |
There was a problem hiding this comment.
Just something like what's in the documentation. I guess it depends what's in the example object.
| if (output_class == "HDF5AnnData") { | ||
| on.exit(cleanup_HDF5AnnData(...)) | ||
| } |
There was a problem hiding this comment.
Should this be outside the error part so the cleanup is still run if one of the later steps fails?
There was a problem hiding this comment.
I think there is no code after this call in the function. The SCE converter is simply a bit limited at this stage
Co-authored-by: Luke Zappia <[email protected]>
