scanpy.Neighbors.compute_eigen

Neighbors.compute_eigen(*, n_comps=15, sort='decrease', rng, sym=None)

Compute eigen decomposition of transition matrix.

Parameters:

n_comps int (default: 15)

Number of eigenvalues/vectors to be computed, set n_comps = 0 if you need all eigenvectors.

rng Generator

Random number generation to control stochasticity.

If a type:SeedLike value, it’s used to seed a new random number generator; If a numpy.random.Generator, rng’s state will be directly advanced; If None, a non-reproducible random number generator is used. See numpy.random.default_rng() for more details.

The default value matches legacy scanpy behavior and will change to None in scanpy 2.0.

Return type:

None

Returns:

Writes the following attributes.

eigen_valuesndarray

Eigenvalues of transition matrix.

eigen_basisndarray

Matrix of eigenvectors (stored in columns). .eigen_basis is projection of data matrix on right eigenvectors, that is, the projection on the diffusion components. these are simply the components of the right eigenvectors and can directly be used for plotting.