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
