Calculate cosine similarity between vector field and cell-neighbor latent state difference. This function matches scTour's cosine_similarity exactly. The calculation borrows the ideas from scvelo.
Usage
cosine_similarity(
zs,
vf,
reverse = FALSE,
n_neigh = 20,
t = NULL,
var_transform = FALSE,
neighbor_indices = NULL
)Arguments
- zs
Latent space matrix (cells x latent_dim)
- vf
Vector field matrix (cells x latent_dim)
- reverse
Whether to reverse vector field direction (default: FALSE)
- n_neigh
Number of neighbors (default: 20)
- t
Time vector for time-aware neighbors (default: NULL)
- var_transform
Variance-stabilizing transformation (default: FALSE)
- neighbor_indices
Pre-computed neighbor indices matrix (optional)