alpha-group-significance: Alpha group significance test and plot¶

Docstring:

Usage: qiime stats alpha-group-significance [OPTIONS]

  Will select between Wilcoxon SRT and Mann-Whitney U depending on the
  presence of repeated measures.

  WARNING:

  This command is deprecated and will be removed in a future version of this
  plugin.

Inputs:
  --i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                          Alpha diversity which will become the "measure"
                                                                    [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple arguments   Sample metadata to use
     will be merged)                                                [required]
  --p-columns TEXT...     Columns to include as group information
    List[Str]                                                       [required]
  --p-subject VALUE Str % Choices('')¹'³ | Str²'⁴
                          If provided, will cause the results to be matched
                          for repeated measures.                 [default: '']
  --p-timepoint VALUE Str % Choices('')¹'² | Str³'⁴
                          If provided, will cause the results to be
                          stratified by timepoint. Required if using
                          ``subject``.                           [default: '']
Outputs:
  --o-distribution ARTIFACT Dist1D[Multi, Independent]¹ | Dist1D[Multi,
    Matched]² | Dist1D[NestedOrdered, Independent]³ | Dist1D[NestedOrdered,
    Matched]⁴             Dist1D generated by metadata and alpha diversity.
                                                                    [required]
  --o-stats ARTIFACT      A stats table of the per-group/timepoint results
    StatsTable[Pairwise]                                            [required]
  --o-raincloud VISUALIZATION
                          A visualization of the distribution and statistics
                                                                    [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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --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: alpha group significance faith pd
  qiime stats alpha-group-significance \
    --i-alpha-diversity alpha-div-faith-pd.qza \
    --m-metadata-file metadata.tsv \
    --p-columns genotype donor_status \
    --p-subject mouse_id \
    --p-timepoint days_post_transplant \
    --o-distribution dist.qza \
    --o-stats stats.qza \
    --o-raincloud raincloud.qzv
  qiime stats alpha-group-significance \
    --i-alpha-diversity alpha-div-faith-pd.qza \
    --m-metadata-file metadata.tsv \
    --p-columns genotype donor_status \
    --o-distribution dist2.qza \
    --o-stats stats2.qza \
    --o-raincloud raincloud2.qzv