Open
Conversation
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
MUCDK
reviewed
Jun 14, 2024
| latent_space_selection: | ||
| Key or Keys which specifies the latent or feature space used for computing the conditional variance. | ||
| A single key has to be a latent space in :attr:`~anndata.AnnData.obsm` or | ||
| a gene in :attr:`~anndata.AnnData.var_names`. |
Collaborator
There was a problem hiding this comment.
a feature in ..., because we might also store proteins/ATAC, etc.
MUCDK
reviewed
Jun 14, 2024
| Key or Keys which specifies the latent or feature space used for computing the conditional variance. | ||
| A single key has to be a latent space in :attr:`~anndata.AnnData.obsm` or | ||
| a gene in :attr:`~anndata.AnnData.var_names`. | ||
| A set of keys has to be a subset of genes in :attr:`~anndata.AnnData.var_names`. |
Collaborator
There was a problem hiding this comment.
Type hinting doesn't say set, but list.
MUCDK
reviewed
Jun 14, 2024
| source: K, | ||
| target: K, | ||
| forward: bool = True, | ||
| latent_space_selection: Union[str, list[str]] = "X_pca", |
Collaborator
There was a problem hiding this comment.
let's not call it latent space. can also be raw space, e.g. gene space. Also, the types are not clear
MUCDK
reviewed
Jun 14, 2024
| mask = [var_name in latent_space_selection for var_name in self.adata.var_names] | ||
| latent_space = self.adata[:, mask].X.toarray() | ||
| else: | ||
| raise KeyError("Unknown latent space selection.") |
Collaborator
There was a problem hiding this comment.
When we have a key error, we want to print what the wrong key is.
MUCDK
reviewed
Jun 14, 2024
Comment on lines
+762
to
+776
| filter_value = source if forward else target | ||
| opposite_filter_value = target if forward else source | ||
|
|
||
| if isinstance(latent_space_selection, str): | ||
| if latent_space_selection in self.adata.obsm: | ||
| latent_space = self.adata.obsm[latent_space_selection] | ||
| elif latent_space_selection in self.adata.var_names: | ||
| latent_space = self.adata[:, latent_space_selection in self.adata.var_names].X.toarray() | ||
| else: | ||
| raise KeyError("Gene/Latent space not found.") | ||
| elif type(latent_space_selection) in [list, np.ndarray]: | ||
| mask = [var_name in latent_space_selection for var_name in self.adata.var_names] | ||
| latent_space = self.adata[:, mask].X.toarray() | ||
| else: | ||
| raise KeyError("Unknown latent space selection.") |
Collaborator
There was a problem hiding this comment.
Let's make this a function (within the function)
MUCDK
reviewed
Jun 14, 2024
| ) | ||
|
|
||
| cond_var = [] | ||
| for i in range(cond_dists.shape[1]): # type: ignore[union-attr] |
MUCDK
reviewed
Jun 14, 2024
|
|
||
| batch_size = batch_size if batch_size is not None else len(df) | ||
| func = self.push if forward else self.pull | ||
| for batch in range(0, len(df), batch_size): |
Collaborator
There was a problem hiding this comment.
why do we actually do this ? :)
MUCDK
reviewed
Jun 14, 2024
| batch_size=batch_size, | ||
| ) | ||
| if key_added is None: | ||
| assert isinstance(out, pd.DataFrame) |
Collaborator
There was a problem hiding this comment.
check for some properties, e.g. no NaN, non-negativity
MUCDK
reviewed
Jun 14, 2024
| @pytest.mark.parametrize("key_added", [None, "test"]) | ||
| @pytest.mark.parametrize("batch_size", [None, 2]) | ||
| @pytest.mark.parametrize("latent_space_selection", ["X_pca", "KLF12", ["KLF12", "Dlip3", "Dref"]]) | ||
| def test_compute_variance_pipeline( |
Collaborator
There was a problem hiding this comment.
also check for raise Error with wrong attributes.
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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.
Added function
compute_variance()as well as a test, similar tocompute_entropy().