SCANVI bug fixes #1458
Merged
SCANVI bug fixes #1458
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## master #1458 +/- ##
==========================================
+ Coverage 90.97% 91.04% +0.06%
==========================================
Files 111 111
Lines 8743 8762 +19
==========================================
+ Hits 7954 7977 +23
+ Misses 789 785 -4
Continue to review full report at Codecov.
|
adamgayoso
requested changes
Mar 23, 2022
| "Unknown", | ||
| batch_key="batch", | ||
| categorical_covariate_keys=["cat1", "cat2"], | ||
| continuous_covariate_keys=["cont1", "cont2"], |
There was a problem hiding this comment.
arches won't actually work as intended with extra categorical covariates. We should not test extra categorical covariates and instead add an error message in load_query_data if they are detected. Extra continuous are fine.
Comment on lines
+84
to
+99
| if ( | ||
| allow_missing_labels | ||
| and self.attr_key is not None | ||
| and self.attr_key not in adata_target.obs | ||
| ): | ||
| # Fill in original .obs attribute with unlabeled_category values. | ||
| warnings.warn( | ||
| f"Missing labels key {self.attr_key}. Filling in with unlabeled category {self._unlabeled_category}." | ||
| ) | ||
| _set_data_in_registry( | ||
| adata_target, | ||
| self._unlabeled_category, | ||
| self.attr_name, | ||
| self._original_attr_key, | ||
| ) | ||
|
|
adamgayoso
approved these changes
Mar 24, 2022
meeseeksmachine
pushed a commit
to meeseeksmachine/scvi-tools
that referenced
this pull request
Mar 24, 2022
adamgayoso
pushed a commit
that referenced
this pull request
Mar 24, 2022
Co-authored-by: Justin Hong <[email protected]>
nrclaudio
pushed a commit
to nrclaudio/scvi-tools-tune
that referenced
this pull request
Jun 21, 2022
* address issue 1449 * fix scanvi covariate handling * fix tests * raise error on extra cat covs * release note
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #1449
Fixes #1450