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scatterplot: Make 2D scatterplot and linear regression of regressor predictions.ΒΆ

Docstring:

Usage: qiime sample-classifier scatterplot [OPTIONS]

  Make a 2D scatterplot and linear regression of predicted vs. true values
  for a set of samples predicted using a sample regressor.

Options:
  --i-predictions ARTIFACT PATH SampleData[RegressorPredictions]
                                  Predicted values to plot on y axis. Must be
                                  predictions of numeric data produced by a
                                  sample regressor.  [required]
  --m-truth-file MULTIPLE FILE    Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata.
                                  [required]
  --m-truth-column MetadataColumn[Numeric]
                                  Column from metadata file or artifact
                                  viewable as metadata. Metadata column (true
                                  values) to plot on x axis.  [required]
  --p-missing-samples [ignore|error]
                                  How to handle missing samples in metadata.
                                  "error" will fail if missing samples are
                                  detected. "ignore" will cause the feature
                                  table and metadata to be filtered, so that
                                  only samples found in both files are
                                  retained.  [default: error]
  --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.sample_classifier.visualizers import scatterplot

Docstring:

Make 2D scatterplot and linear regression of regressor predictions.

Make a 2D scatterplot and linear regression of predicted vs. true values
for a set of samples predicted using a sample regressor.

Parameters
----------
predictions : SampleData[RegressorPredictions]
    Predicted values to plot on y axis. Must be predictions of numeric data
    produced by a sample regressor.
truth : MetadataColumn[Numeric]
    Metadata column (true values) to plot on x axis.
missing_samples : Str % Choices({'error', 'ignore'}), optional
    How to handle missing samples in metadata. "error" will fail if missing
    samples are detected. "ignore" will cause the feature table and
    metadata to be filtered, so that only samples found in both files are
    retained.

Returns
-------
visualization : Visualization