Closed sjspielman closed 2 weeks ago
Should be ready for a real look now! I think the expect_error()
checks are probably overkill, but I had a nice time writing them, so here they are for now. Sorry for the clutter..........!
Should be ready for a real look now! I think the
expect_error()
checks are probably overkill, but I had a nice time writing them, so here they are for now. Sorry for the clutter..........!
Will review after #752 goes in
Did I say 752? I meant #753
Or we can just check that all the args have length 1, and not support args that don't follow that pattern, as I don't think we expect to use anything like that...
I haven't really been able to think of anything better than this... I guess we could also return the cluster_args
list for users to do what they want with, but given that a minority of users (if any) are likely to be in this circumstance, I do think just the straight data frame return is cleaner.
Ready for another look, and in particular interested in your feedback on my docs wording about parameter defaults, and overall wording for cluster_args
length-1 restriction.
I wrote a bit of what I was thinking there, but you will probably want to rewrite it.
I think what you had there was mostly there tbh, so I expanded it a little bit with more specific bluster information but kept most of what you had.
Purpose/implementation Section
Please link to the GitHub issue that this pull request addresses.
Closes #745
What is the goal of this pull request?
This PR adds a function to perform clustering to the
rOpenScPCA
package. There are many file changes, because I've also merged inmain
to stay in sync, but review can focus only on code inpackages/rOpenScPCA
.I'm filing this as a draft to get some initial feedback, and then can implement the rest (including adding more tests, which I know are thin right now!) and mark for review. Here are the main questions I'm looking for feedback on, but of other high-level feedback is welcome :)
resolution
(used by louvain and leiden),objective_function
(used by leiden), andcluster_args
(for anything else). How does this choice feel to you? Prefer to see fewer or more of the algorithm-specific options pulled out as individual arguments?DataFrame
would be better since it store a lot of that info as metadata, but then I felt it might get confusing for users.Author checklists
Check all those that apply. Note that you may find it easier to check off these items after the pull request is actually filed.
Analysis module and review
README.md
has been updated to reflect code changes in this pull request.Reproducibility checklist
Dockerfile
.environment.yml
file.renv.lock
file.