decoupler.pp.get_obsm

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decoupler.pp.get_obsm#

decoupler.pp.get_obsm(adata, key)#

Extracts values stored in .obsm as a new AnnData object.

This allows to reuse scanpy functions to visualise enrichment scores.

Parameters:

  • adata (AnnData) – Annotated data matrix with observations (rows) and features (columns).

  • key (str) – adata.obsm key to use.

Return type:

AnnData

Returns:

New AnnData object with values of the provided key in .obsm in X.

Example

import decoupler as dc

adata, net = dc.ds.toy()
dc.mt.ulm(adata, net, tmin=3)
scores = dc.pp.get_obsm(adata, "score_ulm")
scores
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