scvelo.pp.moments¶
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scvelo.pp.
moments
(data, n_neighbors=30, n_pcs=None, mode='connectivities', method='umap', use_rep=None, use_highly_variable=True, copy=False)¶ Computes moments for velocity estimation.
First-/second-order moments are computed for each cell across its nearest neighbors, where the neighbor graph is obtained from euclidean distances in PCA space.
- data:
AnnData
Annotated data matrix.
- n_neighbors: int (default: 30)
Number of neighbors to use.
- n_pcs: int (default: None)
Number of principal components to use. If not specified, the full space is used of a pre-computed PCA, or 30 components are used when PCA is computed internally.
- mode: ‘connectivities’ or ‘distances’ (default: ‘connectivities’)
Distance metric to use for moment computation.
- method{{‘umap’, ‘hnsw’, ‘sklearn’, None}} (default: ‘umap’)
Method to compute neighbors, only differs in runtime. Connectivities are computed with adaptive kernel width as proposed in Haghverdi et al. 2016 (https://doi.org/10.1038/nmeth.3971).
- use_repNone, ‘X’ or any key for .obsm (default: None)
Use the indicated representation. If None, the representation is chosen automatically: for .n_vars < 50, .X is used, otherwise ‘X_pca’ is used.
- use_highly_variable: bool (default: True)
Whether to use highly variable genes only, stored in .var[‘highly_variable’].
- copy: bool (default: False)
Return a copy instead of writing to adata.
- Returns
Ms (.layers) – dense matrix with first order moments of spliced counts.
Mu (.layers) – dense matrix with first order moments of unspliced counts.
- data: