Fork me on GitHub

first-distances: Compute first distances or distance from baseline between sequential statesΒΆ

Docstring:

Usage: qiime longitudinal first-distances [OPTIONS]

  Calculates first distances between sequential states for samples collected
  from individual subjects sampled repeatedly at two or more states. This
  method is similar to the "first differences" method, except that it
  requires a distance matrix as input and calculates first differences as
  distances between successive states. Outputs a data series of first
  distances for each individual subject at each sequential pair of states,
  labeled by the SampleID of the second state (e.g., paired distances
  between time 0 and time 1 would be labeled by the SampleIDs at time 1).
  This file can be used as input to linear mixed effects models or other
  longitudinal or diversity methods to compare changes in first distances
  across time or among groups of subjects. Also supports distance from
  baseline (or other static comparison state) by setting the "baseline"
  parameter.

Options:
  --i-distance-matrix ARTIFACT PATH DistanceMatrix
                                  Matrix of distances between pairs of
                                  samples.  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. Sample
                                  metadata file containing
                                  individual_id_column.  [required]
  --p-state-column TEXT           Metadata column containing state (time)
                                  variable information.  [required]
  --p-individual-id-column TEXT   Metadata column containing IDs for
                                  individual subjects.  [required]
  --p-baseline FLOAT              A value listed in the state_column metadata
                                  column against which all other states should
                                  be compared. Toggles calculation of static
                                  distances instead of first distances (which
                                  are calculated if no value is given for
                                  baseline). If a "baseline" value is
                                  provided, sample distances at each state are
                                  compared against the baseline state, instead
                                  of the previous state. Must be a value
                                  listed in the state_column.  [optional]
  --p-replicate-handling [drop|random|error]
                                  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]
  --o-first-distances ARTIFACT PATH SampleData[FirstDifferences]
                                  Series of first distances.  [required if not
                                  passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.longitudinal.methods import first_distances

Docstring:

Compute first distances or distance from baseline between sequential states

Calculates first distances between sequential states for samples collected
from individual subjects sampled repeatedly at two or more states. This
method is similar to the "first differences" method, except that it
requires a distance matrix as input and calculates first differences as
distances between successive states. Outputs a data series of first
distances for each individual subject at each sequential pair of states,
labeled by the SampleID of the second state (e.g., paired distances between
time 0 and time 1 would be labeled by the SampleIDs at time 1). This file
can be used as input to linear mixed effects models or other longitudinal
or diversity methods to compare changes in first distances across time or
among groups of subjects. Also supports distance from baseline (or other
static comparison state) by setting the "baseline" parameter.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
baseline : Float, optional
    A value listed in the state_column metadata column against which all
    other states should be compared. Toggles calculation of static
    distances instead of first distances (which are calculated if no value
    is given for baseline). If a "baseline" value is provided, sample
    distances at each state are compared against the baseline state,
    instead of the previous state. Must be a value listed in the
    state_column.
replicate_handling : Str % Choices({'drop', 'error', 'random'}), 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.

Returns
-------
first_distances : SampleData[FirstDifferences]
    Series of first distances.