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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 `__. For
tutorials, bug reports, and R/MATLAB implementations, visit the `PHATE
GitHub page `__. For help
using PHATE, go `here `__.
Parameters
----------
adata
Annotated data matrix.
n_components
number of dimensions in which the data will be embedded
k
number of nearest neighbors on which to build kernel
a
sets decay rate of kernel tails.
If None, alpha decaying kernel is not used
n_landmark
number of landmarks to use in fast PHATE
t
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
Informational distance constant between -1 and 1.
`gamma=1` gives the PHATE log potential, `gamma=0` gives
a square root potential.
n_pca
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
recommended values: 'euclidean' and 'cosine'
Any metric from `scipy.spatial.distance` can be used
distance metric for building kNN graph
mds_dist
recommended values: 'euclidean' and 'cosine'
Any metric from `scipy.spatial.distance` can be used
distance metric for MDS
mds
Selects which MDS algorithm is used for dimensionality reduction.
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
Random seed. Defaults to the global `numpy` random number generator
verbose
If `True` or an `int`/`Verbosity` ≥ 2/`hint`, print status messages.
If `None`, `sc.settings.verbosity` is used.
copy
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
--------
>>> from anndata import AnnData
>>> import scanpy.external as sce
>>> 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 = AnnData(tree_data)
>>> sce.tl.phate(adata, k=5, a=20, t=150)
>>> adata.obsm['X_phate'].shape
(2000, 2)
>>> sce.pl.phate(adata)
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