Ejemplo n.º 1
0
def run_trajectory_analysis(ord_res,
                            metadata_map,
                            trajectory_categories=None,
                            sort_category=None,
                            algorithm='avg',
                            axes=3,
                            weighted=False,
                            window_size=None):
    """Executes the volatility analysis using 'algorithm' on the input data

    Parameters
    ----------
    ord_res : skbio.maths.stats.ordination.OrdinationResults
        The ordination results
    metadata_map : pandas.DataFrame
        The metadata map where index are samples ids and columns are the
        metadata categories
    trajectory_categories : list of str, optional
        A list of metadata categories to use to create the trajectories. If
        None is passed, the trajectories for all metadata categories are
        computed. Default: None, compute all of them.
    sort_category : str, optional
        The metadata category to use to sort the trajectories. Default: None,
        sort by sample id.
    algorithm : str, optional
        The algorithm used to perform the volatility analysis. Default: avg.
    axes : int, optional
        The number of axes to account while doing the trajectory specific
        calculations. Pass 0 to compute all of them. Default: 3
    weighted : bool, optional
        If true, the output is weighted by the space between samples in the
        `sort_category` column
    window_size : int or long, optional
        If `algorithm` is 'wdiff', the window size to use while computing the
        difference

    Returns
    -------
    skbio.maths.gradient.GradientANOVAResults
        The results of running the volatility analysis over the input data

    Raises
    ------
    ValueError
        If `algorithm` is not a recognized.
    """
    coords_dict = {
        sid: coord
        for sid, coord in zip(ord_res.site_ids, ord_res.site)
    }
    coords = pd.DataFrame.from_dict(coords_dict, orient='index')

    if algorithm == 'avg':
        alg = AverageGradientANOVA(coords, ord_res.proportion_explained,
                                   metadata_map, trajectory_categories,
                                   sort_category, axes, weighted)
    elif algorithm == 'trajectory':
        alg = TrajectoryGradientANOVA(coords, ord_res.proportion_explained,
                                      metadata_map, trajectory_categories,
                                      sort_category, axes, weighted)
    elif algorithm == 'diff':
        alg = FirstDifferenceGradientANOVA(coords,
                                           ord_res.proportion_explained,
                                           metadata_map, trajectory_categories,
                                           sort_category, axes, weighted)
    elif algorithm == 'wdiff':
        alg = WindowDifferenceGradientANOVA(
            coords,
            ord_res.proportion_explained,
            metadata_map,
            window_size,
            trajectory_categories=trajectory_categories,
            sort_category=sort_category,
            axes=axes,
            weighted=weighted)
    else:
        raise ValueError("Algorithm %s not recognized" % algorithm)

    return alg.get_trajectories()
Ejemplo n.º 2
0
def run_trajectory_analysis(
    ord_res,
    metadata_map,
    trajectory_categories=None,
    sort_category=None,
    algorithm="avg",
    axes=3,
    weighted=False,
    window_size=None,
):
    """Executes the volatility analysis using 'algorithm' on the input data

    Parameters
    ----------
    ord_res : skbio.maths.stats.ordination.OrdinationResults
        The ordination results
    metadata_map : pandas.DataFrame
        The metadata map where index are samples ids and columns are the
        metadata categories
    trajectory_categories : list of str, optional
        A list of metadata categories to use to create the trajectories. If
        None is passed, the trajectories for all metadata categories are
        computed. Default: None, compute all of them.
    sort_category : str, optional
        The metadata category to use to sort the trajectories. Default: None,
        sort by sample id.
    algorithm : str, optional
        The algorithm used to perform the volatility analysis. Default: avg.
    axes : int, optional
        The number of axes to account while doing the trajectory specific
        calculations. Pass 0 to compute all of them. Default: 3
    weighted : bool, optional
        If true, the output is weighted by the space between samples in the
        `sort_category` column
    window_size : int or long, optional
        If `algorithm` is 'wdiff', the window size to use while computing the
        difference

    Returns
    -------
    skbio.maths.gradient.GradientANOVAResults
        The results of running the volatility analysis over the input data

    Raises
    ------
    ValueError
        If `algorithm` is not a recognized.
    """
    coords_dict = {sid: coord for sid, coord in zip(ord_res.site_ids, ord_res.site)}
    coords = pd.DataFrame.from_dict(coords_dict, orient="index")

    if algorithm == "avg":
        alg = AverageGradientANOVA(
            coords, ord_res.proportion_explained, metadata_map, trajectory_categories, sort_category, axes, weighted
        )
    elif algorithm == "trajectory":
        alg = TrajectoryGradientANOVA(
            coords, ord_res.proportion_explained, metadata_map, trajectory_categories, sort_category, axes, weighted
        )
    elif algorithm == "diff":
        alg = FirstDifferenceGradientANOVA(
            coords, ord_res.proportion_explained, metadata_map, trajectory_categories, sort_category, axes, weighted
        )
    elif algorithm == "wdiff":
        alg = WindowDifferenceGradientANOVA(
            coords,
            ord_res.proportion_explained,
            metadata_map,
            window_size,
            trajectory_categories=trajectory_categories,
            sort_category=sort_category,
            axes=axes,
            weighted=weighted,
        )
    else:
        raise ValueError("Algorithm %s not recognized" % algorithm)

    return alg.get_trajectories()