VisualizeQuartets: Visualize quartet difference on trees, by split

In Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

Visualize quartet difference on trees, by split

Description

Visualize quartet difference on trees, by split

Usage

VisualizeQuartets(
  tree1,
  tree2,
  style = "pie",
  setPar = TRUE,
  precision = 3L,
  Plot = plot.phylo,
  scale = 1L,
  spectrum = viridisLite::viridis(101),
  legend = TRUE,
  ...
)

Arguments

tree1, tree2	Trees of class phylo, with identical leaf labels.
style	Character string specifying split labels with an unambiguous abbreviation of: label: Label stating proportion of resolved quartets in agreement, coloured accordingly; pie: Pie chart showing proportion of quartets in agreement, sized according to number of quartets influenced by each split; bar: Bar showing proportion of quartets in agreement, labelled; size: Circle coloured according to proportion of quartets in agreement, with area corresponding to number of quartet statements associated with split.
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.
scale	Numeric, enlargement factor for split labels.
spectrum	101-element vector specifying a range of colours by which to colour matches.
legend	Logical specifying whether to display simple legend.
...	Additional parameters to send to Plot().

Author(s)

Martin R. Smith ([e-mail])

Examples

library('TreeTools', quietly = TRUE, warn.conflicts = FALSE)
VisualizeQuartets(BalancedTree(10), CollapseNode(PectinateTree(10), 19),
                  style = 'label')
# Keep original plotting parameters:
origPar <- par(mfrow = c(2, 2))
VisualizeQuartets(BalancedTree(10), CollapseNode(PectinateTree(10), 19),
                  setPar = FALSE)
VisualizeQuartets(BalancedTree(10), CollapseNode(PectinateTree(10), 19),
                  style = 'bar', legend = FALSE, setPar = FALSE)
par(origPar)
VisualizeQuartets(BalancedTree(20), CollapseNode(PectinateTree(20), 29:33),
                  style = 'size', scale = 2)

Quartet documentation built on July 8, 2022, 5:08 p.m.