scater argument name update

[antagomir]

The latest development version of the scater package has now switched from exprs_values to assay_name as the argument name, following my recent PR.

I have proposed similar change for scuttle.

It could be expected that the scated update will be added in the Bioc April 2023 devel version.

Action points:

• update mia package family accordingly
• update OMA accordingly

Perhaps good to wait until scuttle update (if it is accepted and happens soon) and Bioc devel in April before implementing these changes, so that all dependencies will work more smoothly.

[antagomir]

scuttle does not support assay_name; they use assay.type (and have interesting reasoning for this); see scuttle issue 21

scater now uses assay_name as we do.

I was checking if scater can consider moving to assay.type but currently unresolved scater issue 189.

If scuttle and scater stick to different names, we will need to decide on this. Interoperability with both packages is useful, so we could support both, but have one as the primary argument. Either way.

Of note: the scuttle maintainer is SingleCellExperiment (SCE) author, and TreeSE inherits SCE. In this sense it would be more logical to shift using similar naming scheme than the SCE ecosystem. This could be checked more systematically for other names on the same go. If the changes would seem to be too big to implement, this can be reconsidered but it could be worth having a look.

[antagomir]

OK, Bioc release is here. We can proceed with this.

Just confirm first that the latest Bioc release indeed includes assay.type argument for scater and scuttle packages.