confusion-matrix: Make a confusion matrix from sample classifier predictions.¶

Docstring:

Usage: qiime sample-classifier confusion-matrix [OPTIONS]

  Make a confusion matrix and calculate accuracy of predicted vs. true values
  for a set of samples classified using a sample classifier. If per-sample
  class probabilities are provided, will also generate Receiver Operating
  Characteristic curves and calculate area under the curve for each class.

Inputs:
  --i-predictions ARTIFACT SampleData[ClassifierPredictions]
                         Predicted values to plot on x axis. Should be
                         predictions of categorical data produced by a sample
                         classifier.                                [required]
  --i-probabilities ARTIFACT SampleData[Probabilities]
                         Predicted class probabilities for each input sample.
                                                                    [optional]
Parameters:
  --m-truth-file METADATA
  --m-truth-column COLUMN  MetadataColumn[Categorical]
                         Metadata column (true values) to plot on y axis.
                                                                    [required]
  --p-missing-samples TEXT Choices('error', 'ignore')
                         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']
  --p-vmin VALUE Float | Str % Choices('auto')
                         The minimum value to use for anchoring the colormap.
                         If "auto", vmin is set to the minimum value in the
                         data.                               [default: 'auto']
  --p-vmax VALUE Float | Str % Choices('auto')
                         The maximum value to use for anchoring the colormap.
                         If "auto", vmax is set to the maximum value in the
                         data.                               [default: 'auto']
  --p-palette TEXT Choices('YellowOrangeBrown', 'YellowOrangeRed',
    'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue',
    'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis',
    'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy',
    'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream',
    'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale')
                         The color palette to use for plotting.
                                                          [default: 'sirocco']
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.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.