bioalpha.singlecell.preprocessing.log1p

bioalpha.singlecell.preprocessing.log1p(data: AnnData | csr_matrix | csc_matrix | ndarray, *, base: Number | None = None, copy: bool = False, chunked: bool = False, chunk_size: int | None = None, layer: str | None = None, obsm: str | None = None, key_added: str | None = None, obs_mask: str | None = None, var_mask: str | None = None, **kwargs) → AnnData | csr_matrix | csc_matrix | ndarray | None

Logarithmize the data matrix.

Computes data = log(data + 1), where log denotes the natural logarithm unless a different base is given.

Parameters:

  • X (Union[AnnData, csr_matrix, csc_matrix, ndarray]) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to genes.

  • base (Optional[Number], default = None) – Base of the logarithm. Natural logarithm is used by default.

  • copy (bool, default = False) – Determines whether a copy is returned.

  • chunked (bool, default = False) – Process the data matrix in chunks, which will save memory.

  • chunk_size (Optional[int], default = None) – n_obs of the chunks to process the data in.

  • layer (Optional[str], default = None) – Entry of layers to tranform.

  • obsm (Optional[str], default = None) – Entry of obsm to transform.

  • key_added (Optional[str], default = filter_genes_mask) – Name of the field in adata.var where the filter array is stored. Only for mapping data.

  • obs_mask (Optional[str], default = None) – If obs_mask is not None, filter cells by adata.obs[obs_mask].

  • var_mask (Optional[str], default = None) – If obs_mask is not None, filter genes by adata.obs[obs_mask].

  • **kwargs – Other parameters passed to BatchReader.

Return type:

Returns or updates data, depending on copy.