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ols-regression: Simplicial Ordinary Least Squares RegressionΒΆ

Docstring:

Usage: qiime gneiss ols-regression [OPTIONS]

  Perform linear regression on balances. This will tell youhow much
  variability is explained by metadata categories in your formula.

Inputs:
  --i-table ARTIFACT FeatureTable[Balance]
                       The feature table containing the samples in which
                       simplicial regression will be performed.     [required]
  --i-tree ARTIFACT    A hierarchy of feature identifiers where each
    Hierarchy          tipcorresponds to the feature identifiers in the table.
                       This tree can contain tip ids that are not present in
                       the table, but all feature ids in the table must be
                       present in this tree.                        [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple          Metadata information that contains the covariates of
     arguments will    interest.
     be merged)                                                     [required]
  --p-formula TEXT     Formula specifying the statistical model. In other
                       words, a list of the metadata categories that will be
                       used in the regression model, typically separated by
                       "+". For more information see
                       https://patsy.readthedocs.io/en/latest/API-reference.ht
                       ml                                           [required]
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 ols_regression

Docstring:

Simplicial Ordinary Least Squares Regression

Perform linear regression on balances. This will tell youhow much
variability is explained by metadata categories in your formula.

Parameters
----------
table : FeatureTable[Balance]
    The feature table containing the samples in which simplicial regression
    will be performed.
tree : Hierarchy
    A hierarchy of feature identifiers where each tipcorresponds to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metadata : Metadata
    Metadata information that contains the covariates of interest.
formula : Str
    Formula specifying the statistical model. In other words, a list of the
    metadata categories that will be used in the regression model,
    typically separated by "+". For more information see
    https://patsy.readthedocs.io/en/latest/API-reference.html

Returns
-------
visualization : Visualization