Add the functions for calculating the bivariate Moran index and the b… #329
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…ivariate local Moran index
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Pull Request Overview
This pull request introduces bivariate spatial correlation functionality to the spateo package by adding two new functions for calculating bivariate Moran's I statistics. The implementation provides both global and local spatial correlation analysis between spatial variables and gene expression data.
- Adds global bivariate Moran's I calculation between spatial variables and genes
- Adds local bivariate Moran's I calculation between any two spatial features
- Integrates the new functions into the tools module's public API
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| spateo/tools/spatial_correlation.py | New module implementing bivariate Moran's I functions with comprehensive parameter validation and result handling |
| spateo/tools/init.py | Exports the new spatial correlation functions to make them available in the public API |
| copy: bool = False, | ||
| ) -> Optional[pd.DataFrame]: | ||
| """ | ||
| Calculate global bivariate Moran's I between a spatial variable and gene expression |
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The docstring incorrectly describes the function as calculating 'global bivariate Moran's I' when the function name and implementation clearly indicate it calculates 'local bivariate Moran's I'. This should be corrected to 'Calculate local bivariate Moran's I between two spatial features'.
| Calculate global bivariate Moran's I between a spatial variable and gene expression | |
| Calculate local bivariate Moran's I between two spatial features |
| feature1_key | ||
| Key in `adata.obs` for the first variable or gene_name | ||
| feature2_key | ||
| Key in `adata.obs` for the seconda variable or gene_name |
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There is a typo in the parameter description: 'seconda' should be 'second'.
| Key in `adata.obs` for the seconda variable or gene_name | |
| Key in `adata.obs` for the second variable or gene_name |
| raise KeyError(f"'{feature1_key}' not found in adata.obs and a gene name") | ||
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| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | ||
| raise KeyError(f"'{feature2_key}' not found in adata.obs and a gene name") |
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The error message is grammatically incorrect and unclear. It should be: "'{feature1_key}' not found in adata.obs or as a gene name".
| raise KeyError(f"'{feature1_key}' not found in adata.obs and a gene name") | |
| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | |
| raise KeyError(f"'{feature2_key}' not found in adata.obs and a gene name") | |
| raise KeyError(f"'{feature1_key}' not found in adata.obs or as a gene name") | |
| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | |
| raise KeyError(f"'{feature2_key}' not found in adata.obs or as a gene name") |
| raise KeyError(f"'{feature1_key}' not found in adata.obs and a gene name") | ||
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| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | ||
| raise KeyError(f"'{feature2_key}' not found in adata.obs and a gene name") |
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The error message is grammatically incorrect and unclear. It should be: "'{feature2_key}' not found in adata.obs or as a gene name".
| raise KeyError(f"'{feature1_key}' not found in adata.obs and a gene name") | |
| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | |
| raise KeyError(f"'{feature2_key}' not found in adata.obs and a gene name") | |
| raise KeyError(f"'{feature1_key}' not found in adata.obs or as a gene name") | |
| if feature2_key not in adata.obs and feature2_key not in adata.var_names: | |
| raise KeyError(f"'{feature2_key}' not found in adata.obs or as a gene name") |
| y = np.array(adata.obs[feature2_key].values, dtype=np.float64) | ||
| else: | ||
| idx = adata.var_names.get_loc(feature2_key) | ||
| print(hasattr(adata.X[:, idx], "toarray")) |
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This debug print statement should be removed from production code as it serves no functional purpose and will clutter the output.
| print(hasattr(adata.X[:, idx], "toarray")) |
2 participants
This pull request introduces two new spatial correlation functions to the spateo package:
spatial_bv_moran_obs_genes: Calculates the bivariate global Moran’s I index for a cell's feature with specificed genes.
spatial_bv_local_moran_obs_genes: Calculates the bivariate local Moran’s I index for any two cell's features.