clone_root

Compute Clone-Level Diffusion Pseudotime

Usage

clone_dpt(
  clone_embedding,
  cell_meta,
  clone_col,
  cluster_col,
  start_cluster,
  k = 10,
  dpt_k = 30
)

Arguments

clone_embedding

A numeric matrix where rows are clones and columns are features.

cell_meta

A data frame of metadata with clone and cluster annotations.

clone_col

Name of the column containing clone identifiers.

cluster_col

Name of the column containing cluster labels.

start_cluster

The cluster label used to select the root clone.

k

Integer. Number of neighbors for kNN graph construction (default: 10).

dpt_k

Integer. Number of eigenvectors for DPT (default: 30).

Value

A numeric vector of clone-level pseudotime values.

Details

Estimates pseudotime on the clone embedding by building a kNN graph and applying diffusion pseudotime from a root clone.

Examples

clone_pt <- clone_dpt(clone_embedding, cell_meta, "clone", "cluster", "Naive")
#> Error in dbscan::kNN(x = x, k = k): object 'clone_embedding' not found
hist(clone_pt)
#> Error in hist(clone_pt): object 'clone_pt' not found