scanpy.pp.pca

scanpy.pp.pca(data, n_comps=None, *, layer=None, zero_center=True, svd_solver=None, random_state=0, return_info=False, mask_var=_empty, use_highly_variable=None, dtype='float32', chunked=False, chunk_size=None, key_added=None, copy=False)

Principal component analysis [Pedregosa et al., 2011].

Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa et al., 2011].

Changed in version 1.5.0: In previous versions, computing a PCA on a sparse matrix would make a dense copy of the array for mean centering. As of scanpy 1.5.0, mean centering is implicit. While results are extremely similar, they are not exactly the same. If you would like to reproduce the old results, pass a dense array.

Parameters:

data AnnData | ndarray | csr_matrix | csc_matrix

The (annotated) data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

n_comps int | None (default: None)

Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation.

layer str | None (default: None)

If provided, which element of layers to use for PCA.

zero_center bool | None (default: True)

If True, compute standard PCA from covariance matrix. If False, omit zero-centering variables (uses scikit-learn TruncatedSVD or dask-ml TruncatedSVD), which allows to handle sparse input efficiently. Passing None decides automatically based on sparseness of the data.

svd_solver Union[Literal['auto', 'full', 'tsqr', 'randomized'], Literal['tsqr', 'randomized'], Literal['auto', 'full', 'randomized'], Literal['arpack', 'covariance_eigh'], Literal['arpack', 'randomized'], Literal['covariance_eigh'], None] (default: None)

SVD solver to use:

None

See chunked and zero_center descriptions to determine which class will be used. Depending on the class and the type of X different values for default will be set. For sparse dask arrays, will use 'covariance_eigh'. If scikit-learn PCA is used, will give 'arpack', if scikit-learn TruncatedSVD is used, will give 'randomized', if dask-ml PCA or IncrementalPCA is used, will give 'auto', if dask-ml TruncatedSVD is used, will give 'tsqr'

'arpack'

for the ARPACK wrapper in SciPy (svds()) Not available with dask arrays.

'covariance_eigh'

Classic eigendecomposition of the covariance matrix, suited for tall-and-skinny matrices. With dask, array must be CSR or dense and chunked as (N, adata.shape[1]).

'randomized'

for the randomized algorithm due to Halko (2009). For dask arrays, this will use svd_compressed().

'auto'

chooses automatically depending on the size of the problem.

'tsqr'

Only available with dense dask arrays. “tsqr” algorithm from Benson et. al. (2013).

Changed in version 1.9.3: Default value changed from 'arpack' to None.

Changed in version 1.4.5: Default value changed from 'auto' to 'arpack'.

Efficient computation of the principal components of a sparse matrix currently only works with the 'arpack’ or 'covariance_eigh’ solver.

If X is a sparse dask array, a custom 'covariance_eigh' solver will be used. If X is a dense dask array, dask-ml classes PCA, IncrementalPCA, or TruncatedSVD will be used. Otherwise their scikit-learn counterparts PCA, IncrementalPCA, or TruncatedSVD will be used.

random_state int | RandomState | None (default: 0)

Change to use different initial states for the optimization.

return_info bool (default: False)

Only relevant when not passing an AnnData: see “Returns”.

mask_var ndarray[tuple[int, ...], dtype[bool]] | str | None | Empty (default: _empty)

To run only on a certain set of genes given by a boolean array or a string referring to an array in var. By default, uses .var['highly_variable'] if available, else everything.

use_highly_variable bool | None (default: None)

Whether to use highly variable genes only, stored in .var['highly_variable']. By default uses them if they have been determined beforehand.

Deprecated since version 1.10.0: Use mask_var instead

layer

Layer of adata to use as expression values.

dtype Union[dtype[Any], None, type[Any], _SupportsDType[dtype[Any]], str, tuple[Any, int], tuple[Any, SupportsIndex | Sequence[SupportsIndex]], list[Any], _DTypeDict, tuple[Any, Any]] (default: 'float32')

Numpy data type string to which to convert the result.

chunked bool (default: False)

If True, perform an incremental PCA on segments of chunk_size. The incremental PCA automatically zero centers and ignores settings of random_seed and svd_solver. Uses sklearn IncrementalPCA or dask-ml IncrementalPCA. If False, perform a full PCA and use sklearn PCA or dask-ml PCA

chunk_size int | None (default: None)

Number of observations to include in each chunk. Required if chunked=True was passed.

key_added str | None (default: None)

If not specified, the embedding is stored as obsm['X_pca'], the loadings as varm['PCs'], and the the parameters in uns['pca']. If specified, the embedding is stored as obsm[key_added], the loadings as varm[key_added], and the the parameters in uns[key_added].

copy bool (default: False)

If an AnnData is passed, determines whether a copy is returned. Is ignored otherwise.

Return type:

AnnData | ndarray | csr_matrix | csc_matrix | None

Returns:

If data is array-like and return_info=False was passed, this function returns the PCA representation of data as an array of the same type as the input array.

Otherwise, it returns None if copy=False, else an updated AnnData object. Sets the following fields:

.obsm['X_pca' | key_added]csr_matrix | csc_matrix | ndarray (shape (adata.n_obs, n_comps))

PCA representation of data.

.varm['PCs' | key_added]ndarray (shape (adata.n_vars, n_comps))

The principal components containing the loadings.

.uns['pca' | key_added]['variance_ratio']ndarray (shape (n_comps,))

Ratio of explained variance.

.uns['pca' | key_added]['variance']ndarray (shape (n_comps,))

Explained variance, equivalent to the eigenvalues of the covariance matrix.