bioalpha.h5ad_map.H5ADMap.diet_subset

H5ADMap.diet_subset(subset_path: Path, X: str | None = 'X', keys: List[str] | None = None, row_index: ndarray | str | None = None, col_index: ndarray | str | None = None, copy: bool | None = True)

Subset an anndata with list of keys request. Obs and var are always kept in the new file.

Parameters:

  • subset_path (str) – path to save new file.

  • X (str, default = X) – matrix using for X in new file, it can be X, layers/... or None.

  • keys (Optional[List[str]], default = None) – features to keep in new file. Ex: “uns”, “obsm”, “obsm/X_pca”, …

  • row_index (Union[np.ndarray, str], default = None) – slice obs index or feature in obs. It must be a bool array.

  • col_index (Union[np.ndarray, str], default = None) – slice var index or feature in var. It must be a bool array.

  • copy (Optional[bool], default = False) – Whether return the H5ADMap or not.

Returns:

A subset H5ADMap, raw_file is save as self._raw_file.

Return type:

If copy