compute_logmap: Compute logmap Compute the logmap centered at one tree for...

In svteichman/TreeVizPackage: Tree Visualization Package

Compute logmap Compute the logmap centered at one tree for all other trees.

Description

Compute logmap Compute the logmap centered at one tree for all other trees.

Usage

compute_logmap(
  cons_path,
  tree_paths,
  jar_path = NULL,
  other_cons_path = NULL,
  add_pendant_branches = FALSE,
  cons_tree = NULL,
  trees_complete = NULL,
  cons_in_tree_paths = FALSE
)

Arguments

cons_path	The file path to the tree to center the log map.
tree_paths	A list of file paths to all other trees.
jar_path	A optional file path to the jar file to compute the log map. Otherwise, the logmap.jar file in the TreeVizPackage repo will be used.
other_cons_path	An optional additional consensus tree to plot.
add_pendant_branches	A boolean. When true, the pendant branch lengths will be added to the log map coordinates.
cons_tree	The consensus tree. This is required when add_pendant_branches = TRUE.
trees_complete	Complete list of trees in a multiPhylo object including the base tree. This is required when add_pendant_branches = TRUE.
cons_in_tree_paths	A logical value, TRUE if the consensus tree is included in the tree paths vector.

Value

A matrix with log map coordinates for all trees.

svteichman/TreeVizPackage documentation built on June 22, 2022, 11:21 p.m.