ehrapy.preprocessing.offset_negative_values

ehrapy.preprocessing.offset_negative_values(adata, layer=None, copy=False)

Offsets negative values into positive ones with the lowest negative value becoming 0.

This is primarily used to enable the usage of functions such as log_norm that do not allow negative values for mathematical or technical reasons.

Parameters:

• adata (AnnData) – AnnData object containing X to normalize values in.

• layer (str) – The layer to offset.

• copy (bool) – Whether to return a modified copy of the AnnData object.

Return type:

AnnData

Returns:

Copy of AnnData object if copy is True.