Refactor llm vii #358
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Refactor llm vii #358
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Contributor
mschwoer
commented
Oct 23, 2024
•
mschwoer
commented
- make link between LLM function definitions and actual functions transparent
- add general dimensionality reduction to DataSet
- simplify some helpers
- slightly refactor llm_integration
- add unit tests for whole LLM module
JuliaS92
reviewed
Nov 8, 2024
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| models, | ||
| index=models.index(st.session_state.get(StateKeys.MODEL_NAME)) | ||
| if current_model is not None | ||
| else 0, |
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key = StateKeys.MODEL_NAME?
JuliaS92
reviewed
Nov 8, 2024
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| if model_before != st.session_state[StateKeys.MODEL_NAME]: | ||
| if current_model != st.session_state[StateKeys.MODEL_NAME]: |
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If this is the intendend behaviour, then why is the config a st.fragment?
JuliaS92
reviewed
Nov 8, 2024
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| def perform_dimensionality_reduction( | ||
| self, method: str, group: Optional[str] = None, circle: bool = False | ||
| ): | ||
| """Generic wrapper for dimensionality reduction methods to be used by LLM. | ||
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| Args: | ||
| method (str): "pca", "tsne", "umap" | ||
| group (str, optional): column in metadata that should be used for coloring. Defaults to None. | ||
| circle (bool, optional): draw circle around each group. Defaults to False. | ||
| """ | ||
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| result = { | ||
| "pca": self.plot_pca, | ||
| "tsne": self.plot_tsne, | ||
| "umap": self.plot_umap, | ||
| }.get(method) | ||
| if result is None: | ||
| raise ValueError(f"Invalid method: {method}") | ||
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| return result(group=group, circle=circle) |
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It would be great to have something similarly simple for the differential analysis longterm.
JuliaS92
reviewed
Nov 8, 2024
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| def test_get_protein_id_multiple_matches(gene_to_prot_map): | ||
| """Test with a gene that appears in multiple compound keys.""" | ||
| result = get_protein_id_for_gene_name("MULTI", gene_to_prot_map) | ||
| assert result == "PROT1;PROT2;PROT3" |
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I think this is the same as test_get_protein_id_compound_key. Actually VCL would be the one matching multiple protein ids.
JuliaS92
approved these changes
Nov 8, 2024
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