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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  A table of abundances.  [required]
  --i-tree ARTIFACT PATH Hierarchy
                                  The tree used to calculate the balances.
                                  [required]
  --i-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  Taxonomy information for the OTUs.
                                  [required]
  --p-balance-name TEXT           Name of the balance to summarize.
                                  [required]
  --p-pseudocount FLOAT           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 FLOAT             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 MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata.
                                  [optional]
  --m-metadata-column MetadataColumn[Categorical | Numeric]
                                  Column from metadata file or artifact
                                  viewable as metadata. Metadata column for
                                  plotting the balance (optional).  [optional]
  --o-visualization VISUALIZATION PATH
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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