scanpy.external.pp.magic

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scanpy.external.pp.magic#

scanpy.external.pp.magic(adata, name_list=None, *, knn=5, decay=1, knn_max=None, t=3, n_pca=100, solver='exact', knn_dist='euclidean', random_state=None, n_jobs=None, verbose=False, copy=None, **kwargs)[source]#

Markov Affinity-based Graph Imputation of Cells (MAGIC) API [van Dijk et al., 2018].

MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold.

The algorithm implemented here has changed primarily in two ways compared to the algorithm described in van Dijk et al. [2018]. Firstly, we use the adaptive kernel described in Moon et al. [2019] for improved stability. Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements.

More information and bug reports here. For help, visit <https://krishnaswamylab.org/get-help>.

Parameters:
adata AnnData

An anndata file with .raw attribute representing raw counts.

name_list Union[Literal['all_genes', 'pca_only'], Sequence[str], None] (default: None)

Denoised genes to return. The default 'all_genes'/None may require a large amount of memory if the input data is sparse. Another possibility is 'pca_only'.

knn int (default: 5)

number of nearest neighbors on which to build kernel.

decay float | None (default: 1)

sets decay rate of kernel tails. If None, alpha decaying kernel is not used.

knn_max int | None (default: None)

maximum number of nearest neighbors with nonzero connection. If None, will be set to 3 * knn.

t Union[Literal['auto'], int] (default: 3)

power to which the diffusion operator is powered. This sets the level of diffusion. If ‘auto’, t is selected according to the Procrustes disparity of the diffused data.

n_pca int | None (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 roughly log(n_samples) time. If None, no PCA is performed.

solver Literal['exact', 'approximate'] (default: 'exact')

Which solver to use. “exact” uses the implementation described in van Dijk et al. [2018]. “approximate” uses a faster implementation that performs imputation in the PCA space and then projects back to the gene space. Note, the “approximate” solver may return negative values.

knn_dist str (default: 'euclidean')

recommended values: ‘euclidean’, ‘cosine’, ‘precomputed’ Any metric from scipy.spatial.distance can be used distance metric for building kNN graph. If ‘precomputed’, data should be an n_samples x n_samples distance or affinity matrix.

random_state int | RandomState | None (default: None)

Random seed. Defaults to the global numpy random number generator.

n_jobs int | None (default: None)

Number of threads to use in training. All cores are used by default.

verbose bool (default: False)

If True or an integer >= 2, print status messages. If None, sc.settings.verbosity is used.

copy bool | None (default: None)

If true, a copy of anndata is returned. If None, copy is True if genes is not 'all_genes' or 'pca_only'. copy may only be False if genes is 'all_genes' or 'pca_only', as the resultant data will otherwise have different column names from the input data.

kwargs

Additional arguments to magic.MAGIC.

Return type:

AnnData | None

Returns:

If copy is True, AnnData object is returned.

If subset_genes is not all_genes, PCA on MAGIC values of cells are stored in adata.obsm['X_magic'] and adata.X is not modified.

The raw counts are stored in .raw attribute of AnnData object.

Examples

>>> import scanpy as sc
>>> import scanpy.external as sce
>>> adata = sc.datasets.paul15()
>>> sc.pp.normalize_per_cell(adata)
>>> sc.pp.sqrt(adata)  # or sc.pp.log1p(adata)
>>> adata_magic = sce.pp.magic(adata, name_list=["Mpo", "Klf1", "Ifitm1"], knn=5)
>>> adata_magic.shape
(2730, 3)
>>> sce.pp.magic(adata, name_list="pca_only", knn=5)
>>> adata.obsm["X_magic"].shape
(2730, 100)
>>> sce.pp.magic(adata, name_list="all_genes", knn=5)
>>> adata.X.shape
(2730, 3451)
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