dialogue: update tutorial for the new pertpy DIALOGUE API#58
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The pertpy DIALOGUE implementation has been rewritten as a faithful port of the R reference (scverse/pertpy#TBD). Key API changes: - `Dialogue(...)` constructor keys: `celltype_key`, `sample_key`, `cell_quality_key`, `n_programs` (was `sample_id`, `celltype_key`, `n_counts_key`, `n_mpcs`). - `dl.run(adata)` runs the full three-phase pipeline (fit_programs / test_celltype_pairs / refine_scores) in place; results live on `adata.obs[mcp_*]`, `adata.obsm["X_dialogue"]`, and `adata.uns["dialogue"]`. - `test_association` -> `test_phenotype_association(adata, condition_key=...)`. - `get_extrema_MCP_genes` -> `find_extreme_score_genes(adata, program="MCP1")` (per-program rather than per all-MCPs). - `get_mlm_mcp_genes` -> `get_program_genes(adata, program=..., celltype=...)`. - `multilevel_modeling` is now part of `dl.run(adata)`; per-gene tables are on `adata.uns["dialogue"]["gene_pvalues"]`. - `plot_split_violins` / `plot_pairplot` are not yet ported; the tutorial inlines seaborn equivalents. Clears all cached cell outputs so the next CI run executes the notebook from scratch.
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The pertpy DIALOGUE implementation has been rewritten as a faithful port of the R reference (scverse/pertpy#TBD). This notebook is updated for the new API:
Dialogue(...)constructor:celltype_key,sample_key,cell_quality_key,n_programs.dl.run(adata)runs the full three-phase pipeline; results live onadata.obs[mcp_*],adata.obsm["X_dialogue"], andadata.uns["dialogue"].test_association->test_phenotype_association(adata, condition_key=...).get_extrema_MCP_genes->find_extreme_score_genes(adata, program="MCP1").get_mlm_mcp_genes->get_program_genes(adata, program=..., celltype=...).plot_split_violins/plot_pairplotare not yet ported; the tutorial inlines seaborn equivalents.