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evaluate-taxonomy: Evaluate expected vs. observed taxonomic assignments

Citations
  • Nicholas A Bokulich, Benjamin D Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A Huttley, and J Gregory Caporaso. Optimizing taxonomic classification of marker-gene amplicon sequences with qiime 2's q2-feature-classifier plugin. Microbiome, 2018.

Docstring:

Usage: qiime quality-control evaluate-taxonomy [OPTIONS]

  This visualizer compares a pair of observed and expected taxonomic
  assignments to calculate precision, recall, and F-measure at each taxonomic
  level, up to maximum level specified by the depth parameter. These metrics
  are calculated at each semicolon-delimited rank. This action is useful for
  comparing the accuracy of taxonomic assignment, e.g., between different
  taxonomy classifiers or other bioinformatics methods. Expected taxonomies
  should be derived from simulated or mock community sequences that have known
  taxonomic affiliations.

Inputs:
  --i-expected-taxa ARTIFACT FeatureData[Taxonomy]
                         Expected taxonomic assignments             [required]
  --i-observed-taxa ARTIFACT FeatureData[Taxonomy]
                         Observed taxonomic assignments             [required]
  --i-feature-table ARTIFACT FeatureTable[RelativeFrequency]
                         Optional feature table containing relative frequency
                         of each feature, used to weight accuracy scores by
                         frequency. Must contain all features found in
                         expected and/or observed taxa. Features found in the
                         table but not the expected/observed taxa will be
                         dropped prior to analysis.                 [optional]
Parameters:
  --p-depth INTEGER      Maximum depth of semicolon-delimited taxonomic ranks
                         to test (e.g., 1 = root, 7 = species for the
                         greengenes reference sequence database).   [required]
  --p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
    'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
    'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow')
                         Color palette to utilize for plotting.
                                                             [default: 'Set1']
  --p-require-exp-ids / --p-no-require-exp-ids
                         Require that all features found in observed taxa
                         must be found in expected taxa or raise error.
                                                               [default: True]
  --p-require-obs-ids / --p-no-require-obs-ids
                         Require that all features found in expected taxa
                         must be found in observed taxa or raise error.
                                                               [default: True]
  --p-sample-id TEXT     Optional sample ID to use for extracting frequency
                         data from feature table, and for labeling accuracy
                         results. If no sample-id is provided, feature
                         frequencies are derived from the sum of all samples
                         present in the feature table.              [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.
  --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.

Import:

from qiime2.plugins.quality_control.visualizers import evaluate_taxonomy

Docstring:

Evaluate expected vs. observed taxonomic assignments

This visualizer compares a pair of observed and expected taxonomic
assignments to calculate precision, recall, and F-measure at each taxonomic
level, up to maximum level specified by the depth parameter. These metrics
are calculated at each semicolon-delimited rank. This action is useful for
comparing the accuracy of taxonomic assignment, e.g., between different
taxonomy classifiers or other bioinformatics methods. Expected taxonomies
should be derived from simulated or mock community sequences that have
known taxonomic affiliations.

Parameters
----------
expected_taxa : FeatureData[Taxonomy]
    Expected taxonomic assignments
observed_taxa : FeatureData[Taxonomy]
    Observed taxonomic assignments
depth : Int
    Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
    root, 7 = species for the greengenes reference sequence database).
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
    Color palette to utilize for plotting.
require_exp_ids : Bool, optional
    Require that all features found in observed taxa must be found in
    expected taxa or raise error.
require_obs_ids : Bool, optional
    Require that all features found in expected taxa must be found in
    observed taxa or raise error.
feature_table : FeatureTable[RelativeFrequency], optional
    Optional feature table containing relative frequency of each feature,
    used to weight accuracy scores by frequency. Must contain all features
    found in expected and/or observed taxa. Features found in the table but
    not the expected/observed taxa will be dropped prior to analysis.
sample_id : Str, optional
    Optional sample ID to use for extracting frequency data from feature
    table, and for labeling accuracy results. If no sample_id is provided,
    feature frequencies are derived from the sum of all samples present in
    the feature table.

Returns
-------
visualization : Visualization