beta-phylogenetic-passthrough: Beta Phylogenetic Passthrough¶

Docstring:

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

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

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples over which
                          beta diversity should be computed.        [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     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]
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: run on one core (by default)
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-metric weighted_normalized_unifrac \
    --o-distance-matrix weighted-normalized-unifrac-dm.qza

  # ### example: to run on n cores, replace 1 here with your preferred integer
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-threads 1 \
    --p-metric weighted_normalized_unifrac \
    --o-distance-matrix weighted-normalized-unifrac-dm.qza

  # ### example: use 'auto' to run on all of host system's available CPU cores
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-threads auto \
    --p-metric weighted_normalized_unifrac \
    --o-distance-matrix weighted-normalized-unifrac-dm.qza

  # ### example: use bypass tips to trade specificity for reduced compute time
  # bypass_tips can be used with any threads setting, but auto may be a good
  # choice if you're trimming run time.
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-metric weighted_normalized_unifrac \
    --p-threads auto \
    --p-bypass-tips \
    --o-distance-matrix weighted-normalized-unifrac-dm.qza

  # ### example: variance adjustment
  # Chang et al's variance adjustment may be applied to any unifrac method by
  # using this passthrough function.
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-metric weighted_unifrac \
    --p-threads auto \
    --p-variance-adjusted \
    --o-distance-matrix var-adj-weighted-unifrac-dm.qza

  # ### example: minimal generalized unifrac
  # Generalized unifrac is passed alpha=1 by default. This is roughly
  # equivalent to weighted normalized unifrac, which method will be used
  # instead, because it is better optimized.
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-metric generalized_unifrac \
    --o-distance-matrix generalized-unifrac-dm.qza

  # ### example: generalized unifrac
  # passing a float between 0 and 1 to 'alpha' gives you control over the
  # importance of sample proportions.
  qiime diversity-lib beta-phylogenetic-passthrough \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-metric generalized_unifrac \
    --p-alpha 0.75 \
    --o-distance-matrix generalized-unifrac-dm.qza