Docstring:
Usage: qiime diversity beta-phylogenetic [OPTIONS]
Computes a user-specified phylogenetic beta diversity metric for all pairs
of samples in a feature table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence] The feature table containing the samples over which
beta diversity should be computed. [required]
--i-phylogeny ARTIFACT Phylogenetic tree containing tip identifiers that
Phylogeny[Rooted] correspond to the feature identifiers in the table.
This tree can contain tip ids that are not present
in the table, but all feature ids in the table must
be present in this tree. [required]
Parameters:
--p-metric TEXT Choices('generalized_unifrac', 'unweighted_unifrac',
'weighted_normalized_unifrac', 'weighted_unifrac')
The beta diversity metric to be computed. [required]
--p-threads NTHREADS The number of CPU threads to use in performing this
calculation. May not exceed the number of available
physical cores. If threads = 'auto', one thread will
be created for each identified CPU core on the host.
[default: 1]
--p-variance-adjusted / --p-no-variance-adjusted
Perform variance adjustment based on Chang et al.
BMC Bioinformatics 2011. Weights distances based on
the proportion of the relative abundance represented
between the samples at a given node under
evaluation. [default: False]
--p-alpha PROPORTION Range(0, 1, inclusive_end=True)
This parameter is only used when the choice of
metric is generalized_unifrac. The value of alpha
controls importance of sample proportions. 1.0 is
weighted normalized UniFrac. 0.0 is close to
unweighted UniFrac, but only if the sample
proportions are dichotomized. [optional]
--p-bypass-tips / --p-no-bypass-tips
In a bifurcating tree, the tips make up about 50%
of the nodes in a tree. By ignoring them,
specificity can be traded for reduced compute time.
This has the effect of collapsing the phylogeny, and
is analogous (in concept) to moving from 99% to 97%
OTUs [default: False]
Outputs:
--o-distance-matrix ARTIFACT
DistanceMatrix The resulting distance matrix. [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.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.diversity.pipelines import beta_phylogenetic
Docstring:
Beta diversity (phylogenetic)
Computes a user-specified phylogenetic beta diversity metric for all pairs
of samples in a feature table.
Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
The feature table containing the samples over which beta diversity
should be computed.
phylogeny : Phylogeny[Rooted]
Phylogenetic tree containing tip identifiers that correspond to the
feature identifiers in the table. This tree can contain tip ids that
are not present in the table, but all feature ids in the table must be
present in this tree.
metric : Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac')
The beta diversity metric to be computed.
threads : Threads, optional
The number of CPU threads to use in performing this calculation. May
not exceed the number of available physical cores. If threads = 'auto',
one thread will be created for each identified CPU core on the host.
variance_adjusted : Bool, optional
Perform variance adjustment based on Chang et al. BMC Bioinformatics
2011. Weights distances based on the proportion of the relative
abundance represented between the samples at a given node under
evaluation.
alpha : Float % Range(0, 1, inclusive_end=True), optional
This parameter is only used when the choice of metric is
generalized_unifrac. The value of alpha controls importance of sample
proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
unweighted UniFrac, but only if the sample proportions are
dichotomized.
bypass_tips : Bool, optional
In a bifurcating tree, the tips make up about 50% of the nodes in a
tree. By ignoring them, specificity can be traded for reduced compute
time. This has the effect of collapsing the phylogeny, and is analogous
(in concept) to moving from 99% to 97% OTUs
Returns
-------
distance_matrix : DistanceMatrix
The resulting distance matrix.
