_Assay.clustered_barcodes¶

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

Hierarchical clustering of barcodes.

If the layer is not provided, the barcodes are returned according to the labels.

If a layer is provided, then further hierarchical clustering is performed based on the values in this layer for each label.

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.
splitbybool: 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

Raises

ValueError: When the shape of orderby is not appropriate
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.

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