pairwise-differences: Paired difference testing and boxplots¶

Docstring:

Usage: qiime longitudinal pairwise-differences [OPTIONS]

  Performs paired difference testing between samples from each subject. Sample
  pairs may represent a typical intervention study (e.g., samples collected
  pre- and post-treatment), paired samples from two different timepoints
  (e.g., in a longitudinal study design), or identical samples receiving
  different treatments. This action tests whether the change in a numeric
  metadata value "metric" differs from zero and differs between groups (e.g.,
  groups of subjects receiving different treatments), and produces boxplots of
  paired difference distributions for each group. Note that "metric" can be
  derived from a feature table or metadata.

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                         Feature table to optionally use for paired
                         comparisons.                               [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata file containing
     arguments will be   individual-id-column.
     merged)                                                        [required]
  --p-metric TEXT        Numerical metadata or artifact column to test.
                                                                    [required]
  --p-state-column TEXT  Metadata column containing state (e.g., Time) across
                         which samples are paired.                  [required]
  --p-state-1 TEXT       Baseline state column value.               [required]
  --p-state-2 TEXT       State column value to pair with baseline.  [required]
  --p-individual-id-column TEXT
                         Metadata column containing subject IDs to use for
                         pairing samples. WARNING: if replicates exist for an
                         individual ID at either state-1 or state-2, that
                         subject will be dropped and reported in standard
                         output by default. Set replicate_handling="random" to
                         instead randomly select one member.        [required]
  --p-group-column TEXT  Metadata column on which to separate groups for
                         comparison                                 [optional]
  --p-parametric / --p-no-parametric
                         Perform parametric (ANOVA and t-tests) or
                         non-parametric (Kruskal-Wallis, Wilcoxon, and
                         Mann-Whitney U tests) statistical tests.
                                                              [default: False]
  --p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
    'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
    'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')
                         Color palette to use for generating boxplots.
                                                             [default: 'Set1']
  --p-replicate-handling TEXT Choices('error', 'random', 'drop')
                         Choose how replicate samples are handled. If
                         replicates are detected, "error" causes method to
                         fail; "drop" will discard all replicated samples;
                         "random" chooses one representative at random from
                         among replicates.                  [default: 'error']
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.