skbio.stats.distance.DistanceMatrix.to_series#

DistanceMatrix.to_series()[source]#

Create a pandas.Series from this DistanceMatrix.

The series will contain distances in condensed form: only distances from one matrix triangle are included, and the diagonal is excluded. The series’ index will be a pd.MultiIndex relating pairs of IDs to distances. The pairs of IDs will be in row-major order with respect to the upper matrix triangle.

To obtain all distances (i.e. both upper and lower matrix triangles and the diagonal), use DistanceMatrix.to_data_frame. To obtain only the distances in condensed form (e.g. for use with SciPy), use DistanceMatrix.condensed_form.

Returns:

pd.Series: pd.Series with pairs of IDs on the index.

See also

to_data_frame
condensed_form
scipy.spatial.distance.squareform

Examples

>>> from skbio import DistanceMatrix
>>> dm = DistanceMatrix([[0, 1, 2, 3],
...                      [1, 0, 4, 5],
...                      [2, 4, 0, 6],
...                      [3, 5, 6, 0]], ids=['a', 'b', 'c', 'd'])
>>> dm.to_series()
a  b    1.0
   c    2.0
   d    3.0
b  c    4.0
   d    5.0
c  d    6.0
dtype: float64