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balance-taxonomy: Balance SummaryΒΆ

Docstring:

Usage: qiime gneiss balance-taxonomy [OPTIONS]

  Visualize the distribution of a single balance and summarize its numerator
  and denominator components.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          A table of abundances.                    [required]
  --i-tree ARTIFACT       The tree used to calculate the balances.
    Hierarchy                                                       [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                          Taxonomy information for the OTUs.        [required]
Parameters:
  --p-balance-name TEXT   Name of the balance to summarize.         [required]
  --p-pseudocount NUMBER  The pseudocount to add to avoid division by zero.
                                                                [default: 0.5]
  --p-taxa-level INTEGER  Level of taxonomy to summarize.         [default: 0]
  --p-n-features INTEGER  The number of features to plot in the proportion
                          plot.                                  [default: 10]
  --p-threshold NUMBER    A threshold to designate discrete categories for a
                          numerical metadata column. This will split the
                          numerical column values into two categories, values
                          below the threshold, and values above the threshold.
                          If not specified, this threshold will default to the
                          mean.                                     [optional]
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical | Numeric]
                          Metadata column for plotting the balance
                          (optional).                               [optional]
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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.gneiss.visualizers import balance_taxonomy

Docstring:

Balance Summary

Visualize the distribution of a single balance and summarize its numerator
and denominator components.

Parameters
----------
table : FeatureTable[Frequency]
    A table of abundances.
tree : Hierarchy
    The tree used to calculate the balances.
taxonomy : FeatureData[Taxonomy]
    Taxonomy information for the OTUs.
balance_name : Str
    Name of the balance to summarize.
pseudocount : Float, optional
    The pseudocount to add to avoid division by zero.
taxa_level : Int, optional
    Level of taxonomy to summarize.
n_features : Int, optional
    The number of features to plot in the proportion plot.
threshold : Float, optional
    A threshold to designate discrete categories for a numerical metadata
    column. This will split the numerical column values into two
    categories, values below the threshold, and values above the threshold.
    If not specified, this threshold will default to the mean.
metadata : MetadataColumn[Categorical | Numeric], optional
    Metadata column for plotting the balance (optional).

Returns
-------
visualization : Visualization