Docstring:
Usage: qiime composition da-barplot [OPTIONS]
Generate bar plot views of ANCOM-BC output. One plot will be present per
column in the ANCOM-BC output. The `significance_threshold`,
`effect_size_threshold` and `feature_ids` filter results are intersected,
such that only features that remain after all three filters have been
applied will be present in the output.
Inputs:
--i-data ARTIFACT FeatureData[DifferentialAbundance]
The ANCOM-BC output to be plotted. [required]
Parameters:
--p-effect-size-label TEXT
Label for effect sizes in `data`. [default: 'lfc']
--p-feature-id-label TEXT
Label for feature ids in `data`. [default: 'id']
--p-error-label TEXT Label for effect size errors in `data`.
[default: 'se']
--p-significance-label TEXT
Label for statistical significance level in `data`.
[default: 'q_val']
--p-significance-threshold PROPORTION Range(0.0, 1.0, inclusive_end=True)
Exclude features with statistical significance level
greater (i.e., less significant) than this threshold.
[default: 1.0]
--p-effect-size-threshold NUMBER
Range(0.0, None) Exclude features with an absolute value of effect
size less than this threshold. [default: 0.0]
--m-feature-ids-file METADATA...
(multiple Exclude features if their ids are not included in
arguments will be this index.
merged) [optional]
--p-level-delimiter TEXT
If feature ids encode hierarchical information,
split the levels when generating feature labels in
the visualization using this delimiter. [optional]
--p-label-limit INTEGER
Set the maximum length that will be viewable for
axis labels. You can set this parameter if your axis
labels are being cut off. [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.composition.visualizers import da_barplot
Docstring:
Differential abundance bar plots
Generate bar plot views of ANCOM-BC output. One plot will be present per
column in the ANCOM-BC output. The `significance_threshold`,
`effect_size_threshold` and `feature_ids` filter results are intersected,
such that only features that remain after all three filters have been
applied will be present in the output.
Parameters
----------
data : FeatureData[DifferentialAbundance]
The ANCOM-BC output to be plotted.
effect_size_label : Str, optional
Label for effect sizes in `data`.
feature_id_label : Str, optional
Label for feature ids in `data`.
error_label : Str, optional
Label for effect size errors in `data`.
significance_label : Str, optional
Label for statistical significance level in `data`.
significance_threshold : Float % Range(0.0, 1.0, inclusive_end=True), optional
Exclude features with statistical significance level greater (i.e.,
less significant) than this threshold.
effect_size_threshold : Float % Range(0.0, None), optional
Exclude features with an absolute value of effect size less than this
threshold.
feature_ids : Metadata, optional
Exclude features if their ids are not included in this index.
level_delimiter : Str, optional
If feature ids encode hierarchical information, split the levels when
generating feature labels in the visualization using this delimiter.
label_limit : Int, optional
Set the maximum length that will be viewable for axis labels. You can
set this parameter if your axis labels are being cut off.
Returns
-------
visualization : Visualization
