calour.experiment.Experiment.normalize_compositional¶

Experiment.normalize_compositional(min_frac=0.05, total=10000, inplace=False)[source]¶

Normalize each sample by ignoring the features with mean>=min_frac in all the experiment

This assumes that the majority of features have less than min_frac mean, and that the majority of features don’t change between samples in a constant direction

Parameters:	min_frac (float, optional) – ignore features with mean (over all samples) >= min_frac. total (int, optional) – The total abundance for the non-excluded features per sample inplace (bool, optional) – False (default) to create a new experiment, True to normalize in place
Returns:	The normalized experiment. Note that all features are normalized (including the ones with mean>=min_frac)
Return type:	Experiment