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Visualize quartet difference on trees, by split

Source: R/VisualizeQuartets.R
VisualizeQuartets.Rd

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().

Value

VisualizeQuartets() invisibly returns a list with two elements, named tree1 and tree2, containing a matrix. Each row corresponds to a split within that tree; columns correspond to:

node

The internal numbering of the node corresponding to each split, as displayed by ape::nodelabels()

N, Q, s, d, r1, r2, u

The status of each quartet relative to that split, as documented in QuartetStatus()

res

The number of quartets resolved by that split, i.e. s + d

same

The proportion of quartets resolved by that node that are resolved in the same manner in the other tree; i.e. s / s + d

Author

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

Examples

library("TreeTools", quietly = TRUE)
# Simple plot
VisualizeQuartets(BalancedTree(10), CollapseNode(PectinateTree(10), 19),
                  style = "label")


# Plot with custom graphical 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)


# Circle size denotes similarity
par(mfrow = c(2, 1), mar = rep(0.1, 4))
vq <- VisualizeQuartets(
  tree1 = BalancedTree(20),
  tree2 = CollapseNode(PectinateTree(20), 29:33),
  style = "size", scale = 2,
  setPar = FALSE # necessary for node labels to align
)
# Manually add custom node labels
percentSame <- paste(round(vq[["tree2"]][, "same"] * 100, 1), "%")
nodelabels(percentSame, vq[["tree2"]][, "node"],
           frame = "n", bg = NA, # No frame or background
           adj = 0.5 # align label
           )

           
# restore original graphical parameters
par(origPar)