update finalMerging example

[yyuandann]

No description provided.

[Copilot]

Pull Request Overview

This PR enhances the cluster‐merging workflow by adding parallel DE computation, optional DataFrame output for marker selection, and refactors the final merging API.

• Introduces return_markers_df and n_jobs parameters across merge_clusters and select_marker_genes with parallelized DE via de_pairs_ebayes_parallel.
• Refactors final_merge to accept list‐based cluster assignments, include parallelization options, and adds a helper to convert cluster dicts to lists.
• Updates example scripts and README to demonstrate the new parameters and usage.

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
transcriptomic_clustering/merging.py	Added return_markers_df/n_jobs params and updated marker‐selection logic
transcriptomic_clustering/markers.py	Extended select_marker_genes signature, return type, and DE parallel call
transcriptomic_clustering/final_merging.py	Refactored final_merge API, signature, docstring, and added helper function
transcriptomic_clustering/filter_known_modes.py	Changed known_modes param to lookup by column name; updated signature logic
transcriptomic_clustering/dimension_reduction.py	Adjusted gene count calculation; potential off‐by‐sum bug
transcriptomic_clustering/de_ebayes.py	Added process_pair and de_pairs_ebayes_parallel for parallel DE
transcriptomic_clustering/init.py	Exposed new functions and final_merge; duplicate import cleanup needed
examples/final_merging_example.py	New example demonstrating final_merge with parallel and marker‐DF options
examples/clustering_example.py	Example script for iterative clustering; missing imports cause NameError
README.md	Documented the examples directory

Comments suppressed due to low confidence (5)

transcriptomic_clustering/markers.py:26

• The docstring for select_marker_genes should be updated to describe the new parameters return_markers_df and n_jobs, and to reflect the updated return type (Union[pd.DataFrame, set]).

    """

transcriptomic_clustering/final_merging.py:97

• The docstring for final_merge should be updated to include the added parameters n_jobs and return_markers_df, and to clarify the new return type (tuple of list of lists and markers).

    """

transcriptomic_clustering/filter_known_modes.py:13

• The docstring should be updated to reflect that known_modes is now expected to be a column name (string) in adata.obs rather than a DataFrame or Series.

        known_modes: Optional[str] = None,

examples/clustering_example.py:7

• The script uses sys.path but sys is not imported; add import sys at the top of the file.

sys.path.insert(1, '/allen/programs/celltypes/workgroups/rnaseqanalysis/dyuan/tool/transcriptomic_clustering/')

examples/clustering_example.py:17

• transcriptomic_clustering module is not imported, so calling transcriptomic_clustering.normalize will raise a NameError; add import transcriptomic_clustering or import normalize directly.

adata=transcriptomic_clustering.normalize(adata)

[Copilot]

Using sum(vidx) will sum the index positions rather than count the number of genes; consider using len(vidx) or vidx_bool.sum() to get the correct gene count.

Suggested change

	n_genes = sum(vidx)
	n_genes = len(vidx)

[Copilot]

Duplicate import of merge_clusters; remove the redundant line to keep the module init.py clean.

Suggested change

from .merging import merge_clusters