omicverse.micro.Beta

omicverse.micro.Beta#

class omicverse.micro.Beta(adata, rarefy_depth=None, seed=0)[source]#

Compute sample × sample distance matrices.

Parameters:

  • adata (AnnData) – Samples × features AnnData with int counts.

  • rarefy_depth (Optional[int] (default: None)) – If set, subsample to this depth before distance calculation (good practice for Bray-Curtis / Jaccard to remove library-size effects). None → use raw counts.

  • seed (int (default: 0)) – Random seed for rarefaction.

__init__(adata, rarefy_depth=None, seed=0)[source]#
Parameters:

  • adata (AnnData)

  • rarefy_depth (Optional[int] (default: None))

  • seed (int (default: 0))

Methods

__init__(adata[, rarefy_depth, seed])

braycurtis([rarefy])

Bray-Curtis dissimilarity matrix (samples × samples).

run([metric, rarefy, tree_key, write_to_obsp])

Compute the distance matrix.
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