Implement `from_Seurat` and `to_Seurat`

[bschilder]

from_Seurat strategy

• [x] Only support single-assays when converting to "AbstractAnnData".
• [x] When a Seurat object has >1 assay, tell the user the Default assay is being used.
• [x] Also allow the user to select which assay they want to use.
• [ ] Alternatively, could store original assay name in uns slot. If the stored assay name is available, use that, if not use the default "RNA".
• [x] Turn each matrix element within the selected assay into layers (counts, data, scaled.data).
• [x] Set X as counts matrix element by default, as you can always normalise/manipulate the data from afterwards. However, allow the user the option of setting X=NULL
• [ ] Enable conversion of obsm slot
• [ ] Enable conversion of varm slot

to_Seurat strategy

• [x] Check names of layers, and if they correspond to canonical Seurat matrix element names (counts, data, scaled.data), assign them accordingly.
• [x] Allow the user to set the assay name. If NULL, will set to Seurat default assay name ("RNA").
• [x] When X is not provided, use first layer as assay data, and the rest as additional assays.
• [x] When neither X nor layers are provided, throw error.
• [x] Enable conversion of obsm slot
• [x] Enable conversion of varm slot

[rcannood]

Sounds good, thanks!

[csangara]

@bschilder @rcannood By the way, I will not have time to work on this anymore before the deadline. You can see what I've done so far in the issue-60-from-seurat-obsm-varm branch. I didn't get to test it very much yet so some parts will probably not work.

[rcannood]

Fixed by #183