embedding2dpt

Compute Diffusion Pseudotime from Embedding

Usage

embedding2dpt(embedding, nn_k, root, dpt_k = 30)

Arguments

embedding

A numeric matrix of embeddings (e.g., UMAP or PCA).

nn_k

Integer. Number of neighbors in the kNN graph.

root

Integer. Index of the root cell.

dpt_k

Integer. Number of eigenvectors used in DPT (default: 30).

Value

A numeric vector of pseudotime values for each row in `embedding`.

Details

Builds a kNN graph from an embedding matrix and computes diffusion pseudotime starting from a root cell.

Examples

mat <- matrix(rnorm(200), ncol = 5)
pt <- embedding2dpt(mat, nn_k = 10, root = 1)