skbio.stats.distance.DistanceMatrix.__getitem__

DistanceMatrix.__getitem__(index)

Slice into dissimilarity data by object ID or numpy indexing.

Extracts data from the dissimilarity matrix by object ID, a pair of IDs, or numpy indexing/slicing.

Parameters:

indexstr, two-tuple of str, or numpy index

index can be one of the following forms: an ID, a pair of IDs, or a numpy index.

If index is a string, it is assumed to be an ID and a numpy.ndarray row vector is returned for the corresponding ID. Note that the ID’s row of dissimilarities is returned, not its column. If the matrix is symmetric, the two will be identical, but this makes a difference if the matrix is asymmetric.

If index is a two-tuple of strings, each string is assumed to be an ID and the corresponding matrix element is returned that represents the dissimilarity between the two IDs. Note that the order of lookup by ID pair matters if the matrix is asymmetric: the first ID will be used to look up the row, and the second ID will be used to look up the column. Thus, dm['a', 'b'] may not be the same as dm['b', 'a'] if the matrix is asymmetric.

Otherwise, index will be passed through to DissimilarityMatrix.data.__getitem__, allowing for standard indexing of a numpy.ndarray (e.g., slicing).

Returns:

ndarray or scalar

Indexed data, where return type depends on the form of index (see description of index for more details).

Raises:

MissingIDError

If the ID(s) specified in index are not in the dissimilarity matrix.

Notes

The lookup based on ID(s) is quick.