plotting fixes #167
plotting fixes #167
Conversation
That way we can rely on AnnData for validation and error handling. Closes scverse#162.
use_raw is now a non-optional boolean. This is consistent with the scanpy API, simplifies our logic a lot and makes the output more predictable. Also implement a gene_symbols argument that specifies a column in .var to use as index (closes scverse#124)
ilan-gold
left a comment
ilan-gold
left a comment
There was a problem hiding this comment.
Didn't get to finish this one and won't be around until next week (or maybe week after since I'll be conferencing most of next week), but generally just more checks on argument validities would be good. Maybe simple "does this error or not" tests.
| x: str | None = None, | ||
| y: str | None = None, | ||
| color: str | Sequence[str] | None = None, | ||
| use_raw: bool | Mapping[str, bool] = False, |
There was a problem hiding this comment.
But how do you indicate this breaking change to users? I'm not familiar with the release process or your promises. I guess you;re not on a major version >=1 yet so it doesn't matter. Is there a changelog?
There was a problem hiding this comment.
That is a good question :) I don't think we ever defined a formal release process, but perhaps @gtca knows more. We do have a changelog in the docs directory, I guess I can add this there.
ilia-kats
force-pushed
the
plot_fixes
branch
3 times, most recently
from
cb715c2 to
4487094
Compare
use_raw cannot be None anymore. This is consistent with the scanpy API and leads to more predictable results. Also add a gene_symbols argument. use_raw, layers, and gene_symbols now support being passed dictionaries specifiying different values for different modalities.
2 participants
This PR attempts to make
.pl.scatterandpl.embeddingmore predictable while simplifying our code and fixing some bugs.use_rawcan no longer beNone, it is eitherTrueorFalse. This is consistent with the scanpy API, leads to more predictable output, and allows us to considerably simplify our code.gene_symbolsis supported, with the same functionality as in scanpy.layer,use_raw, andgene_symbolscan be specified individually for each modality by passing dictionaries.