SpaRCL.expression_denoising#

SpaRCL.expression_denoising(adata, relation_key=None)[source]#

Denoise the gene expression matrix using gene relation matrix.

Parameters:
adata : AnnData

Annotated data matrix.

relation_key : str | NoneOptional[str] (default: None)

If not specified, it looks .uns[‘relation’] for relational contrastive learning settings (default storage place for run_RCL()). If specified, it looks .uns[relation_key] for relational contrastive learning settings.

Return type:

AnnData

Returns:

Returns adata of used genes with the following fields updated.

.X

The denoised gene expression matrix.

.layers[‘original’]

The original gene expression matrix.