Docstring:
Usage: qiime rescript evaluate-taxonomy [OPTIONS]
Compute summary statistics on taxonomy artifact(s) and visualize as
interactive lineplots. Summary statistics include the number of unique
labels, taxonomic entropy, and the number of features that are
(un)classified at each taxonomic level. This action is useful for both
reference taxonomies and classification results. The x-axis in these plots
represents the taxonomic levels present in the input taxonomies so are
labeled numerically instead of by rank, but typically for 7-level taxonomies
these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class, 4 = order,
5 = family, 6 = genus, 7 = species.
Inputs:
--i-taxonomies ARTIFACTS... List[FeatureData[Taxonomy]]
One or more taxonomies to evaluate. [required]
Parameters:
--p-labels TEXT... List of labels to use for labeling evaluation
List[Str] results in the resulting visualization. Inputs are
labeled with labels in the order that each is input.
If there are fewer labels than inputs (or no
labels), unnamed inputs are labeled numerically in
sequential order. Extra labels are ignored.
[optional]
--p-rank-handle-regex TEXT
Regular expression indicating which taxonomic rank
a label belongs to; this handle is stripped from the
label prior to operating on the taxonomy. The net
effect is that ambiguous or empty levels can be
removed prior to comparison, enabling selection of
taxonomies with more complete taxonomic information.
For example, "^[dkpcofgs]__" will recognize
greengenes or silva rank handles. [optional]
Outputs:
--o-taxonomy-stats 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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--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.rescript.pipelines import evaluate_taxonomy
Docstring:
Compute summary statistics on taxonomy artifact(s).
Compute summary statistics on taxonomy artifact(s) and visualize as
interactive lineplots. Summary statistics include the number of unique
labels, taxonomic entropy, and the number of features that are
(un)classified at each taxonomic level. This action is useful for both
reference taxonomies and classification results. The x-axis in these plots
represents the taxonomic levels present in the input taxonomies so are
labeled numerically instead of by rank, but typically for 7-level
taxonomies these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class,
4 = order, 5 = family, 6 = genus, 7 = species.
Parameters
----------
taxonomies : List[FeatureData[Taxonomy]]
One or more taxonomies to evaluate.
labels : List[Str], optional
List of labels to use for labeling evaluation results in the resulting
visualization. Inputs are labeled with labels in the order that each is
input. If there are fewer labels than inputs (or no labels), unnamed
inputs are labeled numerically in sequential order. Extra labels are
ignored.
rank_handle_regex : Str, optional
Regular expression indicating which taxonomic rank a label belongs to;
this handle is stripped from the label prior to operating on the
taxonomy. The net effect is that ambiguous or empty levels can be
removed prior to comparison, enabling selection of taxonomies with more
complete taxonomic information. For example, "^[dkpcofgs]__" will
recognize greengenes or silva rank handles.
Returns
-------
taxonomy_stats : Visualization
