omicverse.micro.Ordinate

omicverse.micro.Ordinate#

class omicverse.micro.Ordinate(adata, dist_key='braycurtis')[source]#

Reduce a sample × sample distance matrix to 2-D / 3-D coords.

Parameters:

  • adata (AnnData) – AnnData with a distance matrix already computed by Beta.run() (stored in adata.obsp[dist_key]).

  • dist_key (str (default: 'braycurtis')) – Key into adata.obsp. Defaults to 'braycurtis'.

__init__(adata, dist_key='braycurtis')[source]#
Parameters:

  • adata (AnnData)

  • dist_key (str (default: 'braycurtis'))

Methods

__init__(adata[, dist_key])

nmds([n, random_state, write_to_obsm])

Non-metric multi-dimensional scaling on the distance matrix.

pcoa([n, write_to_obsm])

Principal coordinates analysis.

proportion_explained()

Eigenvalue proportions from the most recent PCoA call.
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