beta-phylogenetic-meta-passthrough: Beta Phylogenetic Meta Passthrough¶

Docstring:

Usage: qiime diversity-lib beta-phylogenetic-meta-passthrough
           [OPTIONS]

  Computes a distance matrix for all pairs of samples in the set of feature
  table and phylogeny pairs, using the unifrac implementation of the selected
  beta diversity metric.

Inputs:
  --i-tables ARTIFACTS... List[FeatureTable[Frequency]]
                          The feature tables containing the samples over
                          which beta diversity should be computed.  [required]
  --i-phylogenies ARTIFACTS... List[Phylogeny[Rooted]]
                          Phylogenetic trees 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]
Parameters:
  --p-metric TEXT Choices('generalized_unifrac', 'unweighted_unifrac',
    'weighted_normalized_unifrac', 'weighted_unifrac')
                          The beta diversity metric to be computed. [required]
  --p-threads NTHREADS    The number of CPU threads to use in performing this
                          calculation. May not exceed the number of available
                          physical cores. If threads = 'auto', one thread will
                          be created for each identified CPU core on the host.
                                                                  [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 PROPORTION Range(0, 1, inclusive_end=True)
                          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]
  --p-weights NUMBERS...  The weight applied to each tree/table pair. This
    List[Float]           tuple is expected to be in index order with tables
                          and phylogenies. Default is to weight each
                          tree/table pair evenly.                   [optional]
  --p-consolidation TEXT Choices('skipping_missing_matrices',
    'missing_zero', 'missing_one', 'skipping_missing_values')
                          The matrix consolidation method, which determines
                          how the individual distance matrices are aggregated
                                          [default: 'skipping_missing_values']
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix        The resulting distance matrix.            [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this action. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --help                  Show this message and exit.

Examples:
  # ### example: Basic meta unifrac
  # For brevity, these examples are focused on meta-specific parameters. See
  # the documentation for beta_phylogenetic_passthrough for additional
  # relevant information.
  # NOTE: the number of trees and tables must match.
  qiime diversity-lib beta-phylogenetic-meta-passthrough \
    --i-tables feature-table1.qza feature-table2.qza \
    --i-phylogenies phylogeny1.qza phylogeny2.qza \
    --p-metric weighted_normalized_unifrac \
    --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

  # ### example: meta with weights
  # The number of weights must match the number of tables/trees.
  # If meaningful, it is possible to pass the same phylogeny more than once.
  qiime diversity-lib beta-phylogenetic-meta-passthrough \
    --i-tables feature-table1.qza feature-table2.qza \
    --i-phylogenies phylogeny.qza phylogeny.qza \
    --p-metric weighted_normalized_unifrac \
    --p-weights 3.0 42.0 \
    --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

  # ### example: changing the consolidation method
  qiime diversity-lib beta-phylogenetic-meta-passthrough \
    --i-tables feature-table1.qza feature-table2.qza \
    --i-phylogenies phylogeny1.qza phylogeny2.qza \
    --p-metric weighted_normalized_unifrac \
    --p-weights 0.4 0.6 \
    --p-consolidation skipping_missing_values \
    --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza