_Assay.clustered_barcodes#

_Assay.clustered_barcodes(orderby=None, splitby='label', override=False)#

Hierarchical clustering of barcodes.

If orderby is not provided, the ordered barcodes are returned according to splitby. If orderby is provided, then further hierarchical clustering is performed based on the values in it for each unqiue splitby value.

Parameters
orderbystr / np.ndarray

An attribute with at least one dimension equal to the number of barcodes. Uses _Assay.get_attribute() to retrieve the values constrained by row.

splitbystr / np.ndarray

Whether to order the barcodes based on the given labels or not. Only applicable when labels orderby is None. Uses _Assay.get_attribute() to retrieve the values constrained by row. The shape must be equal to (#cells)

overridebool

Continue clustering even if the number of id is greater than 1,000.

Returns
numpy.ndarray

Ordered barcodes

Raises
ValueError

When the splitby is not one-dimensional

Exception

When the number of id in the assay is greater than 1,000. This can take a long time to process, hence denied.

Warning

If the number of id is greater than 1,000 and override is passed.