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da-barplot: Differential abundance bar plotsΒΆ

Docstring:

Usage: qiime composition da-barplot [OPTIONS]

  Generate bar plot views of ANCOM-BC output. One plot will be present per
  column in the ANCOM-BC output. The `significance_threshold`,
  `effect_size_threshold` and `feature_ids` filter results are intersected,
  such that only features that remain after all three filters have been
  applied will be present in the output.

Inputs:
  --i-data ARTIFACT FeatureData[DifferentialAbundance]
                        The ANCOM-BC output to be plotted.          [required]
Parameters:
  --p-effect-size-label TEXT
                        Label for effect sizes in `data`.     [default: 'lfc']
  --p-feature-id-label TEXT
                        Label for feature ids in `data`.       [default: 'id']
  --p-error-label TEXT  Label for effect size errors in `data`.
                                                               [default: 'se']
  --p-significance-label TEXT
                        Label for statistical significance level in `data`.
                                                            [default: 'q_val']
  --p-significance-threshold PROPORTION Range(0.0, 1.0, inclusive_end=True)
                        Exclude features with statistical significance level
                        greater (i.e., less significant) than this threshold.
                                                                [default: 1.0]
  --p-effect-size-threshold NUMBER
    Range(0.0, None)    Exclude features with an absolute value of effect
                        size less than this threshold.          [default: 0.0]
  --m-feature-ids-file METADATA...
    (multiple           Exclude features if their ids are not included in
     arguments will be  this index.
     merged)                                                        [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).
  --example-data PATH   Write example data and exit.
  --citations           Show citations and exit.
  --help                Show this message and exit.

Import:

from qiime2.plugins.composition.visualizers import da_barplot

Docstring:

Differential abundance bar plots

Generate bar plot views of ANCOM-BC output. One plot will be present per
column in the ANCOM-BC output. The `significance_threshold`,
`effect_size_threshold` and `feature_ids` filter results are intersected,
such that only features that remain after all three filters have been
applied will be present in the output.

Parameters
----------
data : FeatureData[DifferentialAbundance]
    The ANCOM-BC output to be plotted.
effect_size_label : Str, optional
    Label for effect sizes in `data`.
feature_id_label : Str, optional
    Label for feature ids in `data`.
error_label : Str, optional
    Label for effect size errors in `data`.
significance_label : Str, optional
    Label for statistical significance level in `data`.
significance_threshold : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Exclude features with statistical significance level greater (i.e.,
    less significant) than this threshold.
effect_size_threshold : Float % Range(0.0, None), optional
    Exclude features with an absolute value of effect size less than this
    threshold.
feature_ids : Metadata, optional
    Exclude features if their ids are not included in this index.

Returns
-------
visualization : Visualization