Implement harmonypy component & make changes to concat #54
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Integration CI @ https://github.com/openpipelines-bio/openpipeline/actions/runs/2969733996 |
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Please merge #55 first! |
* add harmony component * Fix missing imports. * Fix typo in changelog * harmonize integrate/harmony and integrate/harmonypy Co-authored-by: Robrecht Cannoodt <[email protected]>
…the anndata/mudata
DriesSchaumont
commented
Sep 2, 2022
src/integrate/concat/script.py
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| if obs_key_sample_name in sample.obs_keys(): | ||
| logger.info(f'Column .obs["{obs_key_sample_name}"] already exists in sample "{sample_id}". Overriding the value for this column.') | ||
| samples.obs = sample.obs.drop(obs_key_sample_name, axis=1) | ||
| for _, modality in sample.mod.items(): |
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Use for modality in sample.mod.values()
src/integrate/concat/script.py
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| @@ -189,7 +186,7 @@ def set_conflicts(concatenated_data: mu.MuData, | |||
| getattr(mod, conflict_matrix_name)[conflict_name] = conflict_data.sort_index() | |||
| return concatenated_data | |||
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| def concatenate_modalities(modalities: dict[str, anndata.AnnData], | |||
| def concatenate_modalities(sample_ids: tuple[str], modalities: dict[str, list[anndata.AnnData]], | |||
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I think I made a mistake here. A general Iterable[anndata.Anndata] is better here
rcannood
changed the title
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I compared this implementation with the implementation from #55
❯ hyperfine --warmup 1 './target/docker/integrate/harmony/harmony -i mms_with_batch.h5mu -o ./test.h5mu' Benchmark 1: ./target/docker/integrate/harmony/harmony -i mms_with_batch.h5mu -o ./test.h5mu Time (mean ± σ): 25.057 s ± 1.703 s [User: 0.177 s, System: 0.128 s] Range (min … max): 23.303 s … 29.393 s 10 runs❯ hyperfine --warmup 1 './target/docker/integrate/harmonypy/harmonypy -i mms_with_batch.h5mu -o ./test.h5mu' Benchmark 1: ./target/docker/integrate/harmonypy/harmonypy -i mms_with_batch.h5mu -o ./test.h5mu Time (mean ± σ): 6.851 s ± 0.399 s [User: 0.167 s, System: 0.114 s] Range (min … max): 6.364 s … 7.703 s 10 runsdocker stats for
harmonydocker stats for
harmonypy