omicverse.metabol.transform

omicverse.metabol.transform(adata, *, method='log', pseudocount=1.0, stash_raw=True)

Apply a feature-level transformation to adata.X.

Parameters:

• method (Literal['log', 'glog', 'autoscale', 'pareto', 'none'] (default: 'log')) – "log", "glog", "autoscale", "pareto", or "none".

• pseudocount (float (default: 1.0)) – For "log" and "glog". Default 1.0 (the MetaboAnalyst default for concentration data).

• stash_raw (bool (default: True)) – If True, stash the pre-transform matrix in layers['raw'] so later steps (e.g. absolute-value plots) can retrieve it.

Return type:

AnnData