scvi.data.fields.ProteinObsmField#
- class scvi.data.fields.ProteinObsmField(*base_field_args, use_batch_mask=True, batch_field=None, **base_field_kwargs)[source]#
An AnnDataField for an protein data stored in an .obsm field of an AnnData object.
For usage with the TotalVI model. Computes an additional mask which indicates where batches are missing protein data.
- Parameters:
registry_key – Key to register field under in data registry.
obsm_key – Key to access the field in the AnnData .obsm mapping.
use_batch_mask (
bool
(default:True
)) – If True, computes a batch mask over the data for missing protein data. Requiresbatch_key
to be not None.batch_key – Key corresponding to the .obs field where batch indices are stored. Used for computing a batch mask over the data for missing protein data.
colnames_uns_key – Key to access column names corresponding to each column of the .obsm field in the AnnData .uns mapping. Only used when .obsm data is a np.ndarray, not a pd.DataFrame.
is_count_data – If True, checks if the data are counts during validation.
correct_data_format – If True, checks and corrects that the AnnData field is C_CONTIGUOUS and csr if it is dense numpy or sparse respectively.
Attributes table#
The key of the data field within the relevant AnnData attribute. |
|
The name of the AnnData attribute where the data is stored. |
|
Returns True if the field is empty as a function of its kwargs. |
|
The modality key of the data field within the MuData (if applicable). |
|
The key that is referenced by models via a data loader. |
Methods table#
Returns a nested dictionary which describes the mapping to the data field. |
|
|
Returns the requested data as determined by the field for a given AnnData/MuData object. |
|
Get summary stats. |
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Register the field. |
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Transfer the field. |
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Validate the field. |
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View the state registry. |
Attributes#
COLUMN_NAMES_KEY
- ProteinObsmField.COLUMN_NAMES_KEY = 'column_names'#
PROTEIN_BATCH_MASK
- ProteinObsmField.PROTEIN_BATCH_MASK = 'protein_batch_mask'#
attr_key
attr_name
is_empty
mod_key
- ProteinObsmField.mod_key[source]#
The modality key of the data field within the MuData (if applicable).
registry_key
Methods#
get_data_registry
- ProteinObsmField.get_data_registry()[source]#
Returns a nested dictionary which describes the mapping to the data field.
The dictionary is of the form {“mod_key”: mod_key, “attr_name”: attr_name, “attr_key”: attr_key}. This mapping is then combined with the mappings of other fields to make up the data registry.
- Return type:
get_field_data
- ProteinObsmField.get_field_data(adata)[source]#
Returns the requested data as determined by the field for a given AnnData/MuData object.
get_summary_stats
register_field
transfer_field
- ProteinObsmField.transfer_field(state_registry, adata_target, **kwargs)[source]#
Transfer the field.
- Return type:
validate_field
view_state_registry