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classify-samples-from-dist: Run k-nearest-neighbors on a labeled distance matrix.ΒΆ

Docstring:

Usage: qiime sample-classifier classify-samples-from-dist [OPTIO
                                                          NS]

  Run k-nearest-neighbors on a labeled distance matrix. Return cross-
  validated (leave one out) predictions and  accuracy. k = 1 by default

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix     a distance matrix                            [required]
Parameters:
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                       Categorical metadata column to use as prediction
                       target.                                      [required]
  --p-k INTEGER        Number of nearest neighbors                [default: 1]
  --p-palette TEXT Choices('YellowOrangeBrown', 'YellowOrangeRed',
    'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue',
    'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', '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-predictions ARTIFACT SampleData[ClassifierPredictions]
                       leave one out predictions for each sample    [required]
  --o-accuracy-results VISUALIZATION
                       Accuracy results 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.sample_classifier.pipelines import classify_samples_from_dist

Docstring:

Run k-nearest-neighbors on a labeled distance matrix.

Run k-nearest-neighbors on a labeled distance matrix. Return cross-
validated (leave one out) predictions and  accuracy. k = 1 by default

Parameters
----------
distance_matrix : DistanceMatrix
    a distance matrix
metadata : MetadataColumn[Categorical]
    Categorical metadata column to use as prediction target.
k : Int, optional
    Number of nearest neighbors
palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
    The color palette to use for plotting.

Returns
-------
predictions : SampleData[ClassifierPredictions]
    leave one out predictions for each sample
accuracy_results : Visualization
    Accuracy results visualization.