scvelo.pp.moments

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.

Parameters:

  • 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].

  • use_rep (None, ‘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.