Visualize quartet difference on trees, by split

Visualize quartet difference on trees, by split

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

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

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)