VisualizeMatching function

Visualize a matching

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

similarity measure. UTF-8

VisualizeMatching(
  Func,
  tree1,
  tree2,
  setPar = TRUE,
  precision = 3L,
  Plot = plot.phylo,
  matchZeros = TRUE,
  plainEdges = FALSE,
  edge.cex = par("cex"),
  value.cex = edge.cex * 0.8,
  edge.frame = "rect",
  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.cex: Character expansion for edge labels. If FALSE, suppress edge labels.
• value.cex: Character expansion for values on edge labels. If FALSE, values are not displayed.
• edge.frame: Character specifying the kind of frame to be printed around the text of the edge labels. Choose an abbreviation of "rect", "circle", or "none".
• edge.width, edge.color, ...``: Additional parameters to send to Plot().

Returns

VisualizeMatching() invisibly returns the matching of splits between tree1 and tree2 (i.e. Func(tree1, tree2, reportMatching = TRUE))

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.

Examples

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

VisualizeMatching(RobinsonFouldsMatching, tree1, tree2)
matching <- VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2,
                              matchZeros = FALSE)
attributes(matching)

Author(s)

Martin R. Smith

(martin.smith@durham.ac.uk)