<commit_before>"""Embed high-dimensional data using PHATE
"""

from .._settings import settings
from .. import logging as logg


def phate(
        adata,
        n_components=2,
        k=5,
        a=15,
        n_landmark=2000,
        t='auto',
        gamma=1,
        n_pca=100,
        knn_dist='euclidean',
        mds_dist='euclidean',
        mds='metric',
        n_jobs=None,
        random_state=None,
        verbose=None,
        copy=False,
        **kwargs):
    """PHATE [Moon17]_.

    Potential of Heat-diffusion for Affinity-based Trajectory Embedding (PHATE)
    embeds high dimensional single-cell data into two or three dimensions for
    visualization of biological progressions.

    For more information and access to the object-oriented interface, read the
    `PHATE documentation <https://phate.readthedocs.io/>`__.  For
    tutorials, bug reports, and R/MATLAB implementations, visit the `PHATE
    GitHub page <https://github.com/KrishnaswamyLab/PHATE/>`__. For help
    using PHATE, go `here <https://krishnaswamylab.org/get-help>`__.

    Parameters
    ----------
    adata : :class:`~anndata.AnnData`
        Annotated data matrix.
    n_components : `int`, optional (default: 2)
        number of dimensions in which the data will be embedded
    k : `int`, optional (default: 5)
        number of nearest neighbors on which to build kernel
    a : `int`, optional (default: 15)
        sets decay rate of kernel tails.
        If None, alpha decaying kernel is not used
    n_landmark : `int`, optional (default: 2000)
        number of landmarks to use in fast PHATE
    t : `int` or 'auto', optional (default: 'auto')
        power to which the diffusion operator is powered
        sets the level of diffusion. If 'auto', t is selected
        according to the knee point in the Von Neumann Entropy of
        the diffusion operator
    gamma : float, optional, default: 1
        Informational distance constant between -1 and 1.
        `gamma=1` gives the PHATE log potential, `gamma=0` gives
        a square root potential.
    n_pca : `int`, optional (default: 100)
        Number of principal components to use for calculating
        neighborhoods. For extremely large datasets, using
        n_pca < 20 allows neighborhoods to be calculated in
        log(n_samples) time.
    knn_dist : string, optional (default: 'euclidean')
        recommended values: 'euclidean' and 'cosine'
        Any metric from `scipy.spatial.distance` can be used
        distance metric for building kNN graph
    mds_dist : string, optional (default: 'euclidean')
        recommended values: 'euclidean' and 'cosine'
        Any metric from `scipy.spatial.distance` can be used
        distance metric for MDS
    mds : {'classic', 'metric', 'nonmetric'}, optional (default: 'metric')
        Selects which MDS algorithm is used for dimensionality reduction
    n_jobs : `int` or `None`, optional (default: `sc.settings.n_jobs`)
        The number of jobs to use for the computation.
        If `None`, `sc.settings.n_jobs` is used.
        If -1 all CPUs are used. If 1 is given, no parallel computing code is
        used at all, which is useful for debugging.
        For n_jobs below -1, (n_cpus + 1 + n_jobs) are used. Thus for
        n_jobs = -2, all CPUs but one are used
    random_state : `int`, `numpy.RandomState` or `None`, optional (default: `None`)
        Random seed. Defaults to the global `numpy` random number generator
    verbose : `bool`, `int` or `None`, optional (default: `sc.settings.verbosity`)
        If `True` or an integer `>= 2`, print status messages.
        If `None`, `sc.settings.verbosity` is used.
    copy : `bool` (default: `False`)
        Return a copy instead of writing to `adata`.
    kwargs : additional arguments to `phate.PHATE`

    Returns
    -------
    Depending on `copy`, returns or updates `adata` with the following fields.

    **X_phate** : `np.ndarray`, (`adata.obs`, shape=[n_samples, n_components], dtype `float`)
        PHATE coordinates of data.

    Examples
    --------
    >>> import scanpy.api as sc
    >>> import phate
    >>> tree_data, tree_clusters = phate.tree.gen_dla(n_dim=100,
                                                      n_branch=20,
                                                      branch_length=100)
    >>> tree_data.shape
    (2000, 100)
    >>> adata = sc.AnnData(tree_data)
    >>> sc.tl.phate(adata, k=5, a=20, t=150)
    >>> adata.obsm['X_phate'].shape
    (2000, 2)
    >>> sc.pl.phate(adata)
    """
    start = logg.info('computing PHATE')
    adata = adata.copy() if copy else adata
    verbose = settings.verbosity if verbose is None else verbose
    if isinstance(settings.verbosity, (str, int)):
        verbose = _settings_verbosity_greater_or_equal_than(2)
    n_jobs = settings.n_jobs if n_jobs is None else n_jobs
    try:
        import phate
    except ImportError:
        raise ImportError(
            'You need to install the package `phate`: please run `pip install '
            '--user phate` in a terminal.')
    X_phate = phate.PHATE(
        n_components=n_components,
        k=k,
        a=a,
        n_landmark=n_landmark,
        t=t,
        gamma=gamma,
        n_pca=n_pca,
        knn_dist=knn_dist,
        mds_dist=mds_dist,
        mds=mds,
        n_jobs=n_jobs,
        random_state=random_state,
        verbose=verbose,
        **kwargs
    ).fit_transform(adata)
    # update AnnData instance
    adata.obsm['X_phate'] = X_phate  # annotate samples with PHATE coordinates
    logg.info(
        '    finished',
        time=start,
        deep=(
            'added\n'
            "    'X_phate', PHATE coordinates (adata.obsm)"
        ),
    )
    return adata if copy else None
<commit_msg>attempt to fix _settings_verbosity_greater_or_equal_than(2) error<commit_after>"""Embed high-dimensional data using PHATE
"""

from .._settings import settings
from .. import logging as logg


def phate(
        adata,
        n_components=2,
        k=5,
        a=15,
        n_landmark=2000,
        t='auto',
        gamma=1,
        n_pca=100,
        knn_dist='euclidean',
        mds_dist='euclidean',
        mds='metric',
        n_jobs=None,
        random_state=None,
        verbose=None,
        copy=False,
        **kwargs):
    """PHATE [Moon17]_.

    Potential of Heat-diffusion for Affinity-based Trajectory Embedding (PHATE)
    embeds high dimensional single-cell data into two or three dimensions for
    visualization of biological progressions.

    For more information and access to the object-oriented interface, read the
    `PHATE documentation <https://phate.readthedocs.io/>`__.  For
    tutorials, bug reports, and R/MATLAB implementations, visit the `PHATE
    GitHub page <https://github.com/KrishnaswamyLab/PHATE/>`__. For help
    using PHATE, go `here <https://krishnaswamylab.org/get-help>`__.

    Parameters
    ----------
    adata : :class:`~anndata.AnnData`
        Annotated data matrix.
    n_components : `int`, optional (default: 2)
        number of dimensions in which the data will be embedded
    k : `int`, optional (default: 5)
        number of nearest neighbors on which to build kernel
    a : `int`, optional (default: 15)
        sets decay rate of kernel tails.
        If None, alpha decaying kernel is not used
    n_landmark : `int`, optional (default: 2000)
        number of landmarks to use in fast PHATE
    t : `int` or 'auto', optional (default: 'auto')
        power to which the diffusion operator is powered
        sets the level of diffusion. If 'auto', t is selected
        according to the knee point in the Von Neumann Entropy of
        the diffusion operator
    gamma : float, optional, default: 1
        Informational distance constant between -1 and 1.
        `gamma=1` gives the PHATE log potential, `gamma=0` gives
        a square root potential.
    n_pca : `int`, optional (default: 100)
        Number of principal components to use for calculating
        neighborhoods. For extremely large datasets, using
        n_pca < 20 allows neighborhoods to be calculated in
        log(n_samples) time.
    knn_dist : string, optional (default: 'euclidean')
        recommended values: 'euclidean' and 'cosine'
        Any metric from `scipy.spatial.distance` can be used
        distance metric for building kNN graph
    mds_dist : string, optional (default: 'euclidean')
        recommended values: 'euclidean' and 'cosine'
        Any metric from `scipy.spatial.distance` can be used
        distance metric for MDS
    mds : {'classic', 'metric', 'nonmetric'}, optional (default: 'metric')
        Selects which MDS algorithm is used for dimensionality reduction
    n_jobs : `int` or `None`, optional (default: `sc.settings.n_jobs`)
        The number of jobs to use for the computation.
        If `None`, `sc.settings.n_jobs` is used.
        If -1 all CPUs are used. If 1 is given, no parallel computing code is
        used at all, which is useful for debugging.
        For n_jobs below -1, (n_cpus + 1 + n_jobs) are used. Thus for
        n_jobs = -2, all CPUs but one are used
    random_state : `int`, `numpy.RandomState` or `None`, optional (default: `None`)
        Random seed. Defaults to the global `numpy` random number generator
    verbose : `bool`, `int` or `None`, optional (default: `sc.settings.verbosity`)
        If `True` or an integer `>= 2`, print status messages.
        If `None`, `sc.settings.verbosity` is used.
    copy : `bool` (default: `False`)
        Return a copy instead of writing to `adata`.
    kwargs : additional arguments to `phate.PHATE`

    Returns
    -------
    Depending on `copy`, returns or updates `adata` with the following fields.

    **X_phate** : `np.ndarray`, (`adata.obs`, shape=[n_samples, n_components], dtype `float`)
        PHATE coordinates of data.

    Examples
    --------
    >>> import scanpy.api as sc
    >>> import phate
    >>> tree_data, tree_clusters = phate.tree.gen_dla(n_dim=100,
                                                      n_branch=20,
                                                      branch_length=100)
    >>> tree_data.shape
    (2000, 100)
    >>> adata = sc.AnnData(tree_data)
    >>> sc.tl.phate(adata, k=5, a=20, t=150)
    >>> adata.obsm['X_phate'].shape
    (2000, 2)
    >>> sc.pl.phate(adata)
    """
    start = logg.info('computing PHATE')
    adata = adata.copy() if copy else adata
    verbose = settings.verbosity if verbose is None else verbose
    if isinstance(settings.verbosity, (str, int)):
        verbose = verbose if int(verbose) <= 2 else 2
    n_jobs = settings.n_jobs if n_jobs is None else n_jobs
    try:
        import phate
    except ImportError:
        raise ImportError(
            'You need to install the package `phate`: please run `pip install '
            '--user phate` in a terminal.')
    X_phate = phate.PHATE(
        n_components=n_components,
        k=k,
        a=a,
        n_landmark=n_landmark,
        t=t,
        gamma=gamma,
        n_pca=n_pca,
        knn_dist=knn_dist,
        mds_dist=mds_dist,
        mds=mds,
        n_jobs=n_jobs,
        random_state=random_state,
        verbose=verbose,
        **kwargs
    ).fit_transform(adata)
    # update AnnData instance
    adata.obsm['X_phate'] = X_phate  # annotate samples with PHATE coordinates
    logg.info(
        '    finished',
        time=start,
        deep=(
            'added\n'
            "    'X_phate', PHATE coordinates (adata.obsm)"
        ),
    )
    return adata if copy else None

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