Docstring:
Usage: qiime longitudinal pairwise-differences [OPTIONS]
Performs paired difference testing between samples from each subject. Sample
pairs may represent a typical intervention study (e.g., samples collected
pre- and post-treatment), paired samples from two different timepoints
(e.g., in a longitudinal study design), or identical samples receiving
different treatments. This action tests whether the change in a numeric
metadata value "metric" differs from zero and differs between groups (e.g.,
groups of subjects receiving different treatments), and produces boxplots of
paired difference distributions for each group. Note that "metric" can be
derived from a feature table or metadata.
Inputs:
--i-table ARTIFACT FeatureTable[RelativeFrequency]
Feature table to optionally use for paired
comparisons. [optional]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata file containing
arguments will be individual-id-column.
merged) [required]
--p-metric TEXT Numerical metadata or artifact column to test.
[required]
--p-state-column TEXT Metadata column containing state (e.g., Time) across
which samples are paired. [required]
--p-state-1 TEXT Baseline state column value. [required]
--p-state-2 TEXT State column value to pair with baseline. [required]
--p-individual-id-column TEXT
Metadata column containing subject IDs to use for
pairing samples. WARNING: if replicates exist for an
individual ID at either state-1 or state-2, that
subject will be dropped and reported in standard
output by default. Set replicate_handling="random" to
instead randomly select one member. [required]
--p-group-column TEXT Metadata column on which to separate groups for
comparison [optional]
--p-parametric / --p-no-parametric
Perform parametric (ANOVA and t-tests) or
non-parametric (Kruskal-Wallis, Wilcoxon, and
Mann-Whitney U tests) statistical tests.
[default: False]
--p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis')
Color palette to use for generating boxplots.
[default: 'Set1']
--p-replicate-handling TEXT Choices('error', 'random', 'drop')
Choose how replicate samples are handled. If
replicates are detected, "error" causes method to
fail; "drop" will discard all replicated samples;
"random" chooses one representative at random from
among replicates. [default: 'error']
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.longitudinal.visualizers import pairwise_differences
Docstring:
Paired difference testing and boxplots
Performs paired difference testing between samples from each subject.
Sample pairs may represent a typical intervention study (e.g., samples
collected pre- and post-treatment), paired samples from two different
timepoints (e.g., in a longitudinal study design), or identical samples
receiving different treatments. This action tests whether the change in a
numeric metadata value "metric" differs from zero and differs between
groups (e.g., groups of subjects receiving different treatments), and
produces boxplots of paired difference distributions for each group. Note
that "metric" can be derived from a feature table or metadata.
Parameters
----------
metadata : Metadata
Sample metadata file containing individual_id_column.
metric : Str
Numerical metadata or artifact column to test.
state_column : Str
Metadata column containing state (e.g., Time) across which samples are
paired.
state_1 : Str
Baseline state column value.
state_2 : Str
State column value to pair with baseline.
individual_id_column : Str
Metadata column containing subject IDs to use for pairing samples.
WARNING: if replicates exist for an individual ID at either state_1 or
state_2, that subject will be dropped and reported in standard output
by default. Set replicate_handling="random" to instead randomly select
one member.
group_column : Str, optional
Metadata column on which to separate groups for comparison
parametric : Bool, optional
Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional
Color palette to use for generating boxplots.
replicate_handling : Str % Choices('error', 'random', 'drop'), optional
Choose how replicate samples are handled. If replicates are detected,
"error" causes method to fail; "drop" will discard all replicated
samples; "random" chooses one representative at random from among
replicates.
table : FeatureTable[RelativeFrequency], optional
Feature table to optionally use for paired comparisons.
Returns
-------
visualization : Visualization
