VisualizeMatching: Visualise a matching
In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

VisualizeMatching

R Documentation

Visualise a matching

Description

Depict the splits that are matched between two trees using a specified Generalized Robinson–Foulds similarity measure.

Usage

VisualizeMatching(
  Func,
  tree1,
  tree2,
  setPar = TRUE,
  precision = 3L,
  Plot = plot.phylo,
  matchZeros = TRUE,
  plainEdges = FALSE,
  edge.width = 1,
  edge.color = "black",
  ...
)

Arguments

`Func`	Function used to construct tree similarity.
`tree1, tree2`	Trees of class `phylo`, with identical leaf labels.
`setPar`	Logical specifying whether graphical parameters should be set to display trees side by side.
`precision`	Integer specifying number of significant figures to display when reporting matching scores.
`Plot`	Function to use to plot trees.
`matchZeros`	Logical specifying whether to pair splits with zero similarity (`TRUE`), or leave them unpaired (`FALSE`).
`plainEdges`	Logical specifying whether to plot edges with a uniform width and colour (`TRUE`), or whether to draw edge widths according to the similarity of the associated splits (`FALSE`).
`edge.width, edge.color, ...`	Additional parameters to send to `Plot()`.

Details

Note that when visualizing a Robinson–Foulds distance (using Func = RobinsonFouldsMatching), matched splits are assigned a similarity score of 1, which is deducted from the total number of splits to calculate the Robinson–Foulds distance. Unmatched splits thus contribute one to total tree distance.

Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree1 <- TreeTools::BalancedTree(6)
tree2 <- TreeTools::PectinateTree(6)

VisualizeMatching(RobinsonFouldsMatching, tree1, tree2)
VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2, matchZeros = FALSE)

TreeDist documentation built on Oct. 26, 2023, 1:07 a.m.