Alpha rarefaction curves
Generate interactive alpha rarefaction curves by computing rarefactions
between min_depth and max_depth. The number of intermediate depths to
compute is controlled by the steps parameter, with n iterations being
computed at each rarefaction depth. If sample metadata is provided, samples
may be grouped based on distinct values within a metadata column.
Parameters
- table : FeatureTable[Frequency]
- Feature table to compute rarefaction curves from.
- max_depth : Int % Range(1, None)
- The maximum rarefaction depth. Must be greater than min_depth.
- phylogeny : Phylogeny[Rooted], optional
- Optional phylogeny for phylogenetic metrics.
- metrics : Set[Str % Choices('pielou_e', 'simpson_e', 'shannon', 'margalef', 'menhinick', 'brillouin_d', 'mcintosh_e', 'doubles', 'robbins', 'simpson', 'enspie', 'fisher_alpha', 'heip_e', 'singles', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'goods_coverage', 'mcintosh_d', 'faith_pd', 'ace', 'chao1', 'lladser_pe', 'berger_parker_d')], optional
- The metrics to be measured. By default computes observed_otus, shannon,
and if phylogeny is provided, faith_pd.
- metadata : Metadata, optional
- The sample metadata.
- min_depth : Int % Range(1, None), optional
- The minimum rarefaction depth.
- steps : Int % Range(2, None), optional
- The number of rarefaction depths to include between min_depth and
max_depth.
- iterations : Int % Range(1, None), optional
- The number of rarefied feature tables to compute at each step.
Returns
visualization : Visualization