evaluate-composition: Evaluate expected vs. observed taxonomic composition of samples¶

Docstring:

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

  This visualizer compares the feature composition of pairs of observed and
  expected samples containing the same sample ID in two separate feature
  tables. Typically, feature composition will consist of taxonomy
  classifications or other semicolon-delimited feature annotations. Taxon
  accuracy rate, taxon detection rate, and linear regression scores between
  expected and observed observations are calculated at each semicolon-
  delimited rank, and plots of per-level accuracy and observation correlations
  are plotted. A histogram of distance between false positive observations and
  the nearest expected feature is also generated, where distance equals the
  number of rank differences between the observed feature and the nearest
  common lineage in the expected feature. This visualizer is most suitable for
  testing per-run data quality on sequencing runs that contain mock
  communities or other samples with known composition. Also suitable for
  sanity checks of bioinformatics pipeline performance.

Inputs:
  --i-expected-features ARTIFACT FeatureTable[RelativeFrequency]
                         Expected feature compositions              [required]
  --i-observed-features ARTIFACT FeatureTable[RelativeFrequency]
                         Observed feature compositions              [required]
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). [default: 7]
  --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-plot-tar / --p-no-plot-tar
                         Plot taxon accuracy rate (TAR) on score plot. TAR is
                         the number of true positive features divided by the
                         total number of observed features (TAR = true
                         positives / (true positives + false positives)).
                                                               [default: True]
  --p-plot-tdr / --p-no-plot-tdr
                         Plot taxon detection rate (TDR) on score plot. TDR
                         is the number of true positive features divided by
                         the total number of expected features (TDR = true
                         positives / (true positives + false negatives)).
                                                               [default: True]
  --p-plot-r-value / --p-no-plot-r-value
                         Plot expected vs. observed linear regression r value
                         on score plot.                       [default: False]
  --p-plot-r-squared / --p-no-plot-r-squared
                         Plot expected vs. observed linear regression
                         r-squared value on score plot.        [default: True]
  --p-plot-bray-curtis / --p-no-plot-bray-curtis
                         Plot expected vs. observed Bray-Curtis dissimilarity
                         scores on score plot.                [default: False]
  --p-plot-jaccard / --p-no-plot-jaccard
                         Plot expected vs. observed Jaccard distances scores
                         on score plot.                       [default: False]
  --p-plot-observed-features / --p-no-plot-observed-features
                         Plot observed features count on score plot.
                                                              [default: False]
  --p-plot-observed-features-ratio / --p-no-plot-observed-features-ratio
                         Plot ratio of observed:expected features on score
                         plot.                                 [default: True]
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                         Optional sample metadata that maps observed-features
                         sample IDs to expected-features sample IDs.
                                                                    [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.