Allow user selected distance metric for diffusion maps#5
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Allow user selected distance metric for diffusion maps#5
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We ecountered the follwing testing error, which seems to be an
incompatibility of scanpy:
```Python
# Run PCA
if not use_hvg:
n_comps = n_components
else:
l_n_comps = min(1000, ad.n_obs - 1, ad.n_vars - 1)
> sc.pp.pca(ad, n_comps=l_n_comps, mask_var="highly_variable", zero_center=False)
E TypeError: pca() got an unexpected keyword argument 'mask_var'
```
Update `run_magic_imputation` to make setting small values to 0 optional
* Made pygam an optional dependency that can be installed with `pip install palantir[gam]` or `pip install palantir[full]` * Added proper conditional imports and improved error handling for pygam * Enhanced `run_magic_imputation` to return appropriate data types for different inputs * For numpy arrays or csr_matrix inputs, returns sparse matrices by default (sparse=True) * For pandas DataFrames, returns pandas DataFrames * For AnnData objects, stores results in the object and returns sparse matrices by default * Maintained sparse=True as the default for run_magic_imputation for backward compatibility * Added better support for both sparse and dense output formats in `run_magic_imputation` * Fixed circular import issues between modules * Updated code to use direct AnnData imports for newer compatibility * Improved version detection using importlib.metadata with graceful fallbacks * Fixed Series indexing deprecation warnings in early cell detection functions * Standardized documentation with NumPy-style docstrings throughout the codebase * Added comprehensive type hints to improve code quality and IDE support
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Allow the user to pass distance metric for
sc.pp.neighborstopalantir.utils.run_diffusion_maps.The default is stilleuclideanso the default behavior isn't changed.