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
Import:
from qiime2.plugins.stats.pipelines import alpha_group_significance
Docstring:
Alpha group significance test and plot
.. deprecated::
This Pipeline is deprecated and will be removed in a future version of
this plugin.
Will select between Wilcoxon SRT and Mann-Whitney U depending on the
presence of repeated measures.
Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
Alpha diversity which will become the "measure"
metadata : Metadata
Sample metadata to use
columns : List[Str]
Columns to include as group information
subject : Str % Choices('')¹'³ | Str²'⁴, optional
If provided, will cause the results to be matched for repeated
measures.
timepoint : Str % Choices('')¹'² | Str³'⁴, optional
If provided, will cause the results to be stratified by timepoint.
Required if using ``subject``.
Returns
-------
distribution : Dist1D[Multi, Independent]¹ | Dist1D[Multi, Matched]² | Dist1D[NestedOrdered, Independent]³ | Dist1D[NestedOrdered, Matched]⁴
Dist1D generated by metadata and alpha diversity.
stats : StatsTable[Pairwise]
A stats table of the per-group/timepoint results
raincloud : Visualization
A visualization of the distribution and statistics
