Protein.ga#

Protein.ga(attribute: Union[str, numpy.ndarray], constraint: Optional[str] = None, features: Optional[Sequence] = None)#

Retrieve any attribute in the assay

Returns a pd.DataFrame which could either be a row attribute, column attribute, layer or the passed attribute itself.

Parameters
attribute

The attribute to be searched for in the assay.

features:

In case the attribute is a layer or col, then the subset of features to select

constraint
One of the following is accepted.
  1. None

    Contraint is auto-determined.

  2. ‘row’ / ‘r’

    The first dimension must be equal to the number of cells.

  3. ‘col’ / ‘c’

    The second dimension must be equal to the number of ids or the number of features given in the input.

  4. ‘row+col’ / ‘rc’

    The dimension must be exactly (number of cells, number of ids). The layers have this shape.

Returns
pd.DataFrame

The array of the attribute with the given name found in the assay layer, row attributes, or col attributes in that order. If a constraint is provided, the array is reshaped appropriately if possible, otherwise the best possible constraint for the given input is determined. The columns and index are named based on the barcodes, ids, or sequential integers depending on the constraint.

Raises
ValueError

When the attribute is not found or when the constraint is not satisfied.

TypeError

When the attribute is neither a str not an np.ndarray

Notes

In case the constraint can reshape the array into the expected shape then no error will be raised. Eg. An assay with 100 barcodes and 10 ids has a shape (100, 10). When the attribute ‘barcode’ is fetched constrained by ‘col’ it will not raise an error, but rather return a 10x10 dataframe of barcodes.

>>> import missionbio.mosaic as ms
>>> assay = ms.load_example_dataset("3 cell mix").dna[:100, :10]
>>> assay.shape
(100, 10)
>>> attr = assay.get_attribute('barcode', constraint='col')
>>> attr.shape
(10, 10)

Possible expected behavior >>> assay = assay[:, :9] >>> assay.shape (100, 9) >>> attr = assay.get_attribute(‘barcode’, constraint=’col’) ValueError - ‘The given attribute does not have the expected shape nor could be reshaped appropriately.’