skbio.diversity.beta_diversity

skbio.diversity.beta_diversity(metric, counts, ids=None, validate=True, pairwise_func=None, **kwargs)[source]

Compute distances between all pairs of samples

State: Experimental as of 0.4.0.

Parameters:

  • metric (str, callable) – The pairwise distance function to apply. See the scipy pdist docs and the scikit-bio functions linked under See Also for available metrics. Passing metrics as a strings is preferable as this often results in an optimized version of the metric being used.

  • counts (2D array_like of ints or floats or 2D pandas DataFrame) – Matrix containing count/abundance data where each row contains counts of OTUs in a given sample.

  • ids (iterable of strs, optional) – Identifiers for each sample in counts. By default, samples will be assigned integer identifiers in the order that they were provided (where the type of the identifiers will be str).

  • validate (bool, optional) – If False, validation of the input won’t be performed. This step can be slow, so if validation is run elsewhere it can be disabled here. However, invalid input data can lead to invalid results or error messages that are hard to interpret, so this step should not be bypassed if you’re not certain that your input data are valid. See skbio.diversity for the description of what validation entails so you can determine if you can safely disable validation.

  • pairwise_func (callable, optional) – The function to use for computing pairwise distances. This function must take counts and metric and return a square, hollow, 2-D numpy.ndarray of dissimilarities (floats). Examples of functions that can be provided are scipy.spatial.distance.pdist and sklearn.metrics.pairwise_distances. By default, scipy.spatial.distance.pdist will be used.

  • kwargs (kwargs, optional) – Metric-specific parameters.

Returns:

Distances between all pairs of samples (i.e., rows). The number of rows and columns will be equal to the number of rows in counts.

Return type:

skbio.DistanceMatrix

Raises:

See also

skbio.diversity, skbio.diversity.beta, skbio.diversity.get_beta_diversity_metrics, skbio.diversity.alpha_diversity, scipy.spatial.distance.pdist, sklearn.metrics.pairwise_distances