calour.amplicon_experiment.AmpliconExperiment.sort_centroid¶

AmpliconExperiment.sort_centroid(transform=<function log_n>, inplace=False, **kwargs)[source]¶

Sort the features based on the center of mass

Assuming that samples are already sorted by some continuous field (eg pH), this function will sort features based on their center of mass along this field. Specifically, it calculates the center of mass for each feature and sort features by their center of mass.

Keyword Arguments:
Parameters:	transform (callable, optional) – a callable transform on a 2-d matrix. Input and output of transform are `Experiment`. The transform function modifies `Experiment.data` (it is a copy) but not change the dimension of `Experiment.data`. inplace (bool, optional) – False (default) to create a copy True to Replace data in exp kwargs (dict) – additional keyword parameters passed to `transform`.
	steps (list of callable) – each callable is a transformer that takes `Experiment` object as its 1st argument and has a boolean parameter of `inplace`. Each callable should return an `Experiment` object. inplace (bool) – transformation occuring in the original data or a copy kwargs (dict) – keyword arguments to pass to each transformers. The key should be in the form of “<transformer_name>__<param_name>”. For example, “transform(exp: Experiment, steps=[log_n], log_n__n=3)” will set “n” of function “log_n” to 3
Returns:	features sorted by center of mass
Return type:	Experiment