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evaluate-taxonomy: Evaluate expected vs. observed taxonomic assignments¶
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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