Mitocheck analysis

[axiomcura]

This PR adds the buscar results after applying the method to Mitocheck.

This will be merged once #75 is merged.

Note to reviewer

Most of the changes come from the analysis notebooks. The main parts that need review are:

• metric.py
• the 3.mitocheck-analysis folder

Please ignore the cfret analysis for now. I’m not sure why those results appeared after merging #75. I will submit another PR rerunning the cfret analysis to confirm whether any bugs or errors were introduced after the merge.

Also, please don’t focus too much on the 4.cpjump1-analysis folder, as that analysis is still in progress.

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Pull request overview

This PR adds Mitocheck Buscar analysis outputs (notebooks/scripts + generated plots/tables) and updates core utility/metric code used by the analysis workflows.

Changes:

• Extend shuffle_feature_profiles and add an ENSG→gene-symbol helper for Mitocheck preprocessing.
• Refactor/extend buscar.metrics scoring + EMD threading controls used by downstream analyses.
• Add Mitocheck analysis runner scripts plus converted notebooks and plot-generation R scripts/artifacts.

Reviewed changes

Copilot reviewed 30 out of 54 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
utils/data_utils.py	Adds label shuffling option and ENSG→gene symbol API helper used in Mitocheck workflows.
r_buscar_env.yaml	Expands environment with Python runtime + core Python deps used in Buscar workflows.
notebooks/4.cpjump1-analysis/nbconverted/5.cpjump_u2os_MoA_analysis.py	Removes converted notebook script (analysis reshuffling/cleanup).
notebooks/4.cpjump1-analysis/nbconverted/3.calculate-on-off-scores.py	Removes converted notebook script (analysis reshuffling/cleanup).
notebooks/4.cpjump1-analysis/nbconverted/2.run_buscar_rankings_base_on_moa.py	Updates MoA ranking workflow to new shuffling + metrics API.
notebooks/4.cpjump1-analysis/nbconverted/2.assess-heterogeneity.py	Removes converted notebook script (analysis reshuffling/cleanup).
notebooks/4.cpjump1-analysis/nbconverted/1.generate-on-off-signatures.py	Minor notebook export tweaks and output changes.
notebooks/4.cpjump1-analysis/3.calculate-on-off-scores.ipynb	Removes notebook.
notebooks/4.cpjump1-analysis/2.run_buscar_rankings_base_on_moa.ipynb	Adds updated notebook version of MoA ranking run.
notebooks/4.cpjump1-analysis/2.assess-heterogeneity.ipynb	Removes notebook.
notebooks/4.cpjump1-analysis/1.generate-on-off-signatures.ipynb	Updates to use buscar.signatures.get_signatures and refreshes outputs.
notebooks/3.mitocheck-analysis/run-mitocheck-buscar.sh	Adds a shell entrypoint to nbconvert + run Mitocheck Python analysis scripts.
notebooks/3.mitocheck-analysis/plots/run-mitocheck-plots.sh	Adds a shell entrypoint to nbconvert + run Mitocheck R plotting scripts.
notebooks/3.mitocheck-analysis/plots/nbconverted/1.heat-map-on-off-scores.r	Adds R script to render Mitocheck heatmaps.
notebooks/3.mitocheck-analysis/plots/nbconverted/2.gene-ranking-relationship.r	Adds R script to quantify/correlate rank consistency across phenotypic states.
notebooks/3.mitocheck-analysis/plots/nbconverted/3.linear-modeling-ranking-and-proportion.r	Adds R script for rank vs. phenotype-proportion modeling/plots.
notebooks/3.mitocheck-analysis/plots/all-plots/gene-ranking-relationships/profile_specificity_real.csv	Adds generated summary table artifact.
notebooks/3.mitocheck-analysis/plots/all-plots/gene-ranking-relationships/profile_specificity_real_vs_shuffled.csv	Adds generated comparison summary artifact.
notebooks/3.mitocheck-analysis/plots/all-plots/gene-ranking-relationships/kendall_w_real_permutation_summary.csv	Adds generated Kendall’s W permutation summary artifact.
notebooks/3.mitocheck-analysis/plots/all-plots/gene-ranking-relationships/kendall_w_real_shuffled_permutation_summary.csv	Adds generated real vs shuffled Kendall’s W summary artifact.
notebooks/3.mitocheck-analysis/nbconverted/0.explore-mitocheck-data.py	Adds converted Mitocheck EDA script.
notebooks/3.mitocheck-analysis/nbconverted/1.buscar-analysis.py	Adds converted Mitocheck Buscar analysis (including LOGO evaluation).
notebooks/3.mitocheck-analysis/1.buscar-analysis.ipynb	Adds the Mitocheck analysis notebook source.
notebooks/2.cfret-analysis/4.assess-signature-significance.ipynb	Notebook markdown/content adjustments.
notebooks/2.cfret-analysis/3.generate-pca-umap-components.ipynb	Notebook output changes (cell counts).
notebooks/2.cfret-analysis/1.cfret-pilot-buscar-analysis.ipynb	Notebook metadata version change.
notebooks/0.download-data/2.preprocessing.ipynb	Uses ENSG→symbol conversion + stores mapping for Mitocheck.
buscar/metrics.py	Refactors score computation and adds EMD threading + optional normalization behavior.
.pre-commit-config.yaml	Updates Ruff pre-commit revision.

Comments suppressed due to low confidence (1)

notebooks/4.cpjump1-analysis/nbconverted/2.run_buscar_rankings_base_on_moa.py:377

• measure_phenotypic_activity is invoked with emd_n_threads, but the function signature uses n_threads. As written, this will raise TypeError: unexpected keyword argument 'emd_n_threads'. Update the call site to use n_threads (or align the API if emd_n_threads is intended).

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[wli51]

Great work and nice looking results. LGTM!

[wli51]

what is the dashed line meaning here?

[wli51]

these roc for cpjump looked a lot better!

[axiomcura]

thanks for the review @wli51