def setup_anndata(
cls,
adata: AnnData,
layer: Optional[str] = None,
**kwargs,
):
"""
%(summary)s.
Parameters
----------
%(param_layer)s
"""
setup_method_args = cls._get_setup_method_args(**locals())
# add index for each cell (provided to pyro plate for correct minibatching)
adata.obs["_indices"] = np.arange(adata.n_obs).astype("int64")
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, layer, is_count_data=True),
NumericalObsField(REGISTRY_KEYS.INDICES_KEY, "_indices"),
]
adata_manager = AnnDataManager(
fields=anndata_fields, setup_method_args=setup_method_args
)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)
def setup_anndata(
cls,
adata: AnnData,
batch_key: Optional[str] = None,
labels_key: Optional[str] = None,
categorical_covariate_keys: Optional[List[str]] = None,
continuous_covariate_keys: Optional[List[str]] = None,
layer: Optional[str] = None,
**kwargs,
):
"""
%(summary)s.
Parameters
----------
%(param_batch_key)s
%(param_labels_key)s
%(param_layer)s
%(param_cat_cov_keys)s
%(param_cont_cov_keys)s
"""
setup_method_args = cls._get_setup_method_args(**locals())
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, layer, is_count_data=True),
CategoricalObsField(REGISTRY_KEYS.BATCH_KEY, batch_key),
CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, labels_key),
CategoricalJointObsField(REGISTRY_KEYS.CAT_COVS_KEY,
categorical_covariate_keys),
NumericalJointObsField(REGISTRY_KEYS.CONT_COVS_KEY,
continuous_covariate_keys),
]
adata_manager = AnnDataManager(fields=anndata_fields,
setup_method_args=setup_method_args)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)
def setup_anndata(
cls,
adata: AnnData,
labels_key: Optional[str] = None,
layer: Optional[str] = None,
**kwargs,
):
"""
%(summary)s.
Parameters
----------
%(param_labels_key)s
%(param_layer)s
"""
setup_method_args = cls._get_setup_method_args(**locals())
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, layer, is_count_data=True),
CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, labels_key),
]
adata_manager = AnnDataManager(
fields=anndata_fields, setup_method_args=setup_method_args
)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)
def generic_setup_adata_manager(
adata: AnnData,
batch_key: Optional[str] = None,
labels_key: Optional[str] = None,
categorical_covariate_keys: Optional[List[str]] = None,
continuous_covariate_keys: Optional[List[str]] = None,
layer: Optional[str] = None,
protein_expression_obsm_key: Optional[str] = None,
protein_names_uns_key: Optional[str] = None,
) -> AnnDataManager:
batch_field = CategoricalObsField(REGISTRY_KEYS.BATCH_KEY, batch_key)
anndata_fields = [
batch_field,
LayerField(REGISTRY_KEYS.X_KEY, layer, is_count_data=True),
CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, labels_key),
CategoricalJointObsField(REGISTRY_KEYS.CAT_COVS_KEY,
categorical_covariate_keys),
NumericalJointObsField(REGISTRY_KEYS.CONT_COVS_KEY,
continuous_covariate_keys),
]
if protein_expression_obsm_key is not None:
anndata_fields.append(
ProteinObsmField(
REGISTRY_KEYS.PROTEIN_EXP_KEY,
protein_expression_obsm_key,
use_batch_mask=True,
batch_key=batch_field.attr_key,
colnames_uns_key=protein_names_uns_key,
is_count_data=True,
))
adata_manager = AnnDataManager(fields=anndata_fields)
adata_manager.register_fields(adata)
return adata_manager
def _create_indices_adata_manager(adata: AnnData) -> AnnDataManager:
# add index for each cell (provided to pyro plate for correct minibatching)
adata.obs["_indices"] = np.arange(adata.n_obs).astype("int64")
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, None, is_count_data=True),
CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, None),
NumericalObsField(REGISTRY_KEYS.INDICES_KEY, "_indices"),
]
adata_manager = AnnDataManager(fields=anndata_fields)
adata_manager.register_fields(adata)
return adata_manager
def setup_anndata(
cls,
adata: AnnData,
**kwargs,
) -> Optional[AnnData]:
setup_method_args = cls._get_setup_method_args(**locals())
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, None, is_count_data=True),
]
adata_manager = AnnDataManager(fields=anndata_fields,
setup_method_args=setup_method_args)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)
def setup_anndata(
cls,
adata: AnnData,
**kwargs,
) -> Optional[AnnData]:
setup_method_args = cls._get_setup_method_args(**locals())
# add index for each cell (provided to pyro plate for correct minibatching)
adata.obs["_indices"] = np.arange(adata.n_obs).astype("int64")
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, None, is_count_data=True),
CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, None),
NumericalObsField(REGISTRY_KEYS.INDICES_KEY, "_indices"),
]
adata_manager = AnnDataManager(fields=anndata_fields,
setup_method_args=setup_method_args)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)
def setup_anndata(
cls,
adata: AnnData,
protein_expression_obsm_key: str,
protein_names_uns_key: Optional[str] = None,
batch_key: Optional[str] = None,
layer: Optional[str] = None,
size_factor_key: Optional[str] = None,
categorical_covariate_keys: Optional[List[str]] = None,
continuous_covariate_keys: Optional[List[str]] = None,
**kwargs,
) -> Optional[AnnData]:
"""
%(summary)s.
Parameters
----------
%(param_adata)s
protein_expression_obsm_key
key in `adata.obsm` for protein expression data.
protein_names_uns_key
key in `adata.uns` for protein names. If None, will use the column names of `adata.obsm[protein_expression_obsm_key]`
if it is a DataFrame, else will assign sequential names to proteins.
%(param_batch_key)s
%(param_layer)s
%(param_size_factor_key)s
%(param_cat_cov_keys)s
%(param_cont_cov_keys)s
%(param_copy)s
Returns
-------
%(returns)s
"""
setup_method_args = cls._get_setup_method_args(**locals())
batch_field = CategoricalObsField(REGISTRY_KEYS.BATCH_KEY, batch_key)
anndata_fields = [
LayerField(REGISTRY_KEYS.X_KEY, layer, is_count_data=True),
CategoricalObsField(
REGISTRY_KEYS.LABELS_KEY,
None), # Default labels field for compatibility with TOTALVAE
batch_field,
NumericalObsField(REGISTRY_KEYS.SIZE_FACTOR_KEY,
size_factor_key,
required=False),
CategoricalJointObsField(REGISTRY_KEYS.CAT_COVS_KEY,
categorical_covariate_keys),
NumericalJointObsField(REGISTRY_KEYS.CONT_COVS_KEY,
continuous_covariate_keys),
ProteinObsmField(
REGISTRY_KEYS.PROTEIN_EXP_KEY,
protein_expression_obsm_key,
use_batch_mask=True,
batch_key=batch_field.attr_key,
colnames_uns_key=protein_names_uns_key,
is_count_data=True,
),
]
adata_manager = AnnDataManager(fields=anndata_fields,
setup_method_args=setup_method_args)
adata_manager.register_fields(adata, **kwargs)
cls.register_manager(adata_manager)