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beta-phylogenetic: Beta diversity (phylogenetic)

Citations

[diversity:beta-phylogenetic:CLS11]Qin Chang, Yihui Luan, and Fengzhu Sun. Variance adjusted weighted unifrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC bioinformatics, 12(1):118, 2011. doi:https://doi.org/10.1186/1471-2105-12-118.
[diversity:beta-phylogenetic:CBC+12]Jun Chen, Kyle Bittinger, Emily S Charlson, Christian Hoffmann, James Lewis, Gary D Wu, Ronald G Collman, Frederic D Bushman, and Hongzhe Li. Associating microbiome composition with environmental covariates using generalized unifrac distances. Bioinformatics, 28(16):2106–2113, 2012. doi:10.1093/bioinformatics/bts342.
[diversity:beta-phylogenetic:LK05]Catherine Lozupone and Rob Knight. Unifrac: a new phylogenetic method for comparing microbial communities. Applied and environmental microbiology, 71(12):8228–8235, 2005. doi:10.1128/AEM.71.12.8228-8235.2005.
[diversity:beta-phylogenetic:LHKK07]Catherine A Lozupone, Micah Hamady, Scott T Kelley, and Rob Knight. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Applied and environmental microbiology, 73(5):1576–1585, 2007. doi:10.1128/AEM.01996-06.
[diversity:beta-phylogenetic:MVBK+18]Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez, and Rob Knight. Striped unifrac: enabling microbiome analysis at unprecedented scale. Nature Methods, 2018. doi:10.1038/s41592-018-0187-8.

Docstring:

Usage: qiime diversity beta-phylogenetic [OPTIONS]

  Computes a user-specified phylogenetic beta diversity metric for all pairs
  of samples in a feature table.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  The feature table containing the samples
                                  over which beta diversity should be
                                  computed.  [required]
  --i-phylogeny ARTIFACT PATH Phylogeny[Rooted]
                                  Phylogenetic tree containing tip identifiers
                                  that correspond to the feature identifiers
                                  in the table. This tree can contain tip ids
                                  that are not present in the table, but all
                                  feature ids in the table must be present in
                                  this tree.  [required]
  --p-metric [unweighted_unifrac|weighted_normalized_unifrac|generalized_unifrac|weighted_unifrac]
                                  The beta diversity metric to be computed.
                                  [required]
  --p-n-jobs INTEGER              The number of workers to use.  [default: 1]
  --p-variance-adjusted / --p-no-variance-adjusted
                                  Perform variance adjustment based on Chang
                                  et al. BMC Bioinformatics 2011. Weights
                                  distances based on the proportion of the
                                  relative abundance represented between the
                                  samples at a given node under evaluation.
                                  [default: False]
  --p-alpha FLOAT                 This parameter is only used when the choice
                                  of metric is generalized_unifrac. The value
                                  of alpha controls importance of sample
                                  proportions. 1.0 is weighted normalized
                                  UniFrac. 0.0 is close to unweighted UniFrac,
                                  but only if the sample proportions are
                                  dichotomized.  [optional]
  --p-bypass-tips / --p-no-bypass-tips
                                  In a bifurcating tree, the tips make up
                                  about 50% of the nodes in a tree. By
                                  ignoring them, specificity can be traded for
                                  reduced compute time. This has the effect of
                                  collapsing the phylogeny, and is analogous
                                  (in concept) to moving from 99% to 97% OTUs
                                  [default: False]
  --o-distance-matrix ARTIFACT PATH DistanceMatrix % Properties(['phylogenetic'])
                                  The resulting distance matrix.  [required if
                                  not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.diversity.methods import beta_phylogenetic

Docstring:

Beta diversity (phylogenetic)

Computes a user-specified phylogenetic beta diversity metric for all pairs
of samples in a feature table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which beta diversity
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metric : Str % Choices({'generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'})
    The beta diversity metric to be computed.
n_jobs : Int, optional
    The number of workers to use.
variance_adjusted : Bool, optional
    Perform variance adjustment based on Chang et al. BMC Bioinformatics
    2011. Weights distances based on the proportion of the relative
    abundance represented between the samples at a given node under
    evaluation.
alpha : Float % Range(0, 1, inclusive_end=True), optional
    This parameter is only used when the choice of metric is
    generalized_unifrac. The value of alpha controls importance of sample
    proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
    unweighted UniFrac, but only if the sample proportions are
    dichotomized.
bypass_tips : Bool, optional
    In a bifurcating tree, the tips make up about 50% of the nodes in a
    tree. By ignoring them, specificity can be traded for reduced compute
    time. This has the effect of collapsing the phylogeny, and is analogous
    (in concept) to moving from 99% to 97% OTUs

Returns
-------
distance_matrix : DistanceMatrix % Properties(['phylogenetic'])
    The resulting distance matrix.