omicverse.pp.log1p

omicverse.pp.log1p(adata, *, base=None, copy=False, chunked=False, chunk_size=None, layer=None, obsm=None)[source]

Log-transform expression values with log(1 + x).

Parameters:

  • adata (AnnData) – AnnData object containing expression values.

  • base (Number, optional) – Logarithm base. Uses natural logarithm when None.

  • copy (bool, default=False) – If True, return a transformed copy instead of modifying in place.

  • chunked (bool, default=False) – Whether to transform adata.X by chunks for memory efficiency.

  • chunk_size (int, optional) – Number of cells per chunk when chunked=True.

  • layer (str, optional) – Layer name to transform instead of adata.X.

  • obsm (str, optional) – adata.obsm key to transform instead of adata.X.

Returns:

Returns a transformed AnnData when copy=True; otherwise modifies adata in place and returns None.

Return type:

AnnData or None