Fix heatmap passing of uns data to scanpy.pl.heatmap #110
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
Remove unnecessary existence test and copying of adata.uns[f"{groupby}_colors"] from chromosome_heatmap (tmp_adata.uns was already equal to adata.uns).
In chromosome_heatmap_summary, copy adata.uns to tmp_adata.uns. This prevents scanpy.pl.heatmap from recomputing dendrogram data when tmp_adata is passed with dendrogram=True.
for more information, see https://pre-commit.ci
Explicitly set type of tmp_obs.index to str to avoid anndata ImplicitModificationWarning.
|
I've also explicitly set |
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Outdated suggestions cannot be applied.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.
In
chromosome_heatmap, remove unnecessary existence test and copying ofadata.uns[f"{groupby}_colors"]totmp_adata.uns(which was already defined to be equal toadata.unsin PR #72).In
chromosome_heatmap_summary, settmp_adata.unsequal toadata.unsat definition, just as inchromosome_heatmap, and remove unnecessary test, as above. This preventsscanpy.pl.heatmapfrom issuing adendrogram data not foundwarning and recomputing dendrogram whentmp_adatais passed withdendrogram=True.