scvelo.pp.moments¶

scvelo.pp.
moments
(data, n_neighbors=30, n_pcs=None, mode='connectivities', method='umap', use_rep=None, copy=False)¶ Computes moments for velocity estimation.
First and secondorder 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 precomputed 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’, ‘gauss’, ‘hnsw’, ‘sklearn’, None}} (default: ‘umap’)
Use ‘umap’ [McInnes18] or ‘gauss’ (Gauss kernel following [Coifman05] with adaptive width [Haghverdi16]) for computing connectivities.
 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.
 copy : bool (default: False)
Return a copy instead of writing to adata.
Returns:  Returns or updates adata with the attributes
 Ms (.layers) – dense matrix with first order moments of spliced counts.
 Mu (.layers) – dense matrix with first order moments of unspliced counts.
 data :