Function reference

All functions

P_example

Example genotype probability matrix

P_small

Smaller example genotype probability matrix

annotate_tree()

Find maximum lilkelihood assignment of mutations on a tree

get_mut_graph()

Convert a single-cell phylogeny with mutation placements into a mutation graph

gtree_small

Smaller example annotated tree built from P_small

ladderize()

From ape; will remove once new ape version is released https://github.com/emmanuelparadis/ape/issues/54

mut_nodes_small

Mutation placements calculated from tree_small and P_small

mut_to_tree()

Transfer mutation assignment onto a single-cell phylogeny

perform_nni()

Maximum likelihood tree search via NNI

plot_phylo_heatmap()

Plot phylogeny and mutation heatmap

run_scistree()

Run the scistree workflow

score_tree()

Score a tree based on maximum likelihood

to_phylo()

Convert the phylogeny from tidygraph to phylo object modified from R package alakazam, converts a tbl_graph to a phylo object

tree_small

Smaller example tree built from P_small

tree_upgma

Example tree built using UPGMA from P_small