get_gtree {numbat}

Get a tidygraph tree with simplified mutational history.

Description

Specify either max_cost or n_cut. max_cost works similarly as h and n_cut works similarly as k in stats::cutree. The top-level normal diploid clone is always included.

Usage

get_gtree(tree, P, n_cut = 0, max_cost = 0)

Arguments

tree

phylo Single-cell phylogenetic tree

P

matrix Genotype probability matrix

n_cut

integer Number of cuts on the phylogeny to define subclones

max_cost

numeric Likelihood threshold to collapse internal branches

Value

tbl_graph Phylogeny annotated with branch lengths and mutation events