spatialtis.spatial_heterogeneity

class spatialtis.spatial_heterogeneity(data, method='leibovici', d=None, cut=None, order=False, **kwargs)[source]

Evaluate tissue heterogeneity based on entropy

Entropy describes the amount of information.

  • Shannon entropy (No spatial info included): To compare the difference within a group (eg. different samples from same tumor), Kullback–Leibler divergences for each sample within the group are computed, smaller value indicates less difference within group.

  • Leibovici entropy: You can specific the distance threshold to determine co-occurrence events.

  • Altieri entropy: You can specific the distance interval to determine co-occurrence events.

Parameters

  • data (anndata._core.anndata.AnnData) – AnnData object to perform analysis

  • method (Optional[str]) – “shannon”, “leibovici” and “altieri” (Default: “leibovici”)

  • d (Optional[int]) – method="leibovici", The distance threshold to determine co-occurrence events

  • cut (Optional[Union[int, List, Tuple, pandas.core.series.Series, numpy.ndarray]]) – method="altieri", Distance interval

  • **kwargs – Pass to spatialtis.abc.AnalysisBase

  • order (bool) –

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