CZI-tiledb SCVI Custom Dataloader additions #1339
Open
+426
−3
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
CHANGED TO MAKE IT RUN ON SCVI-TOOLS
ebezzi
reviewed
Jan 31, 2025
| label_keys | ||
| List of obs column names concatenated to form the label column. | ||
| unlabeled_category | ||
| Value used for unlabeled cells in `labels_key` used to set up CZI datamodule with scvi. |
There was a problem hiding this comment.
Suggested change
| Value used for unlabeled cells in `labels_key` used to set up CZI datamodule with scvi. | |
| Value used for unlabeled cells in `labels_key` used to set up `CensusSCVIDataModule`. |
| @@ -577,7 +579,7 @@ def __init__( | |||
| experimental | |||
| """ | |||
| self.exp_uri = experiment.uri | |||
| self.aws_region = experiment.context.tiledb_ctx.config().get("vfs.s3.region") | |||
| self.aws_region = experiment.context.tiledb_ctx#.config().get("vfs.s3.region") | |||
There was a problem hiding this comment.
This seems a bit suspicious - can you remind me what exactly required this change?
|
|
||
| # basicaly we should mimiC everything below to any model census in scvi | ||
| adata_orig = synthetic_iid() | ||
| scvi.model.SCVI.setup_anndata(adata_orig, batch_key="batch") |
There was a problem hiding this comment.
Can you explain a bit what synthetic_iid() generates?
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Outdated suggestions cannot be applied.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.
Adding the SCVI-Tools team addition to the Ebezzi/census branch scvi datamodule from cellxgene.