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.

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix       Matrix of distances between pairs of samples.
                                                                    [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata file containing
     arguments will be   individual-id-column.
     merged)                                                        [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 NUMBER    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 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-first-distances ARTIFACT SampleData[FirstDifferences]
                         Series of first distances.                 [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).
  --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('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.

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