Plot tree differences on ternary plots — QuartetPoints • Quartet

Generate points to depict tree difference (in terms of resolution and accuracy) on a ternary plot, per Smith (2019) .

QuartetPoints(trees, cf = trees[[1]])

SplitPoints(trees, cf = trees[[1]])

BipartitionPoints(trees, cf = trees[[1]])

Arguments

trees: A list of trees of class phylo, with identically labelled tips.
cf: Comparison tree of class phylo. If unspecified, each tree is compared to the first tree in trees.

Value

A data frame listing the ternary coordinates of trees, based on the amount of information that they have in common with the comparison tree (which defaults to the first member of the list, if unspecified).

Details

The ternary plot (produced using the Ternary package, Smith 2017 ) will depict the number of quartets or splits that are:

resolved in the reference tree (cf), but neither present nor contradicted in each comparison tree (trees);
resolved differently in the reference and the comparison tree;
resolved in the same manner in the reference and comparison trees.

If the reference tree (cf) is taken to represent the best possible knowledge of the "true" topology, then polytomies in the reference tree represent uncertainty. If a tree in trees resolves relationships within this polytomy, it is not possible to establish (based only on the reference tree) whether this resolution is correct or erroneous. As such, extra resolution in trees that is neither corroborated nor contradicted by cf is ignored.

References

Smith MR (2017). “Ternary: An R Package for Creating Ternary Plots.” doi:10.5281/zenodo.1068997 .

Smith MR (2019). “Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets.” Biology Letters, 15(2), 20180632. doi:10.1098/rsbl.2018.0632 .

Author

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

Examples

library("Ternary")
data("sq_trees")

TernaryPlot(alab = "Unresolved", blab = "Contradicted", clab = "Consistent",
            point = "right")
TernaryLines(list(c(0, 2/3, 1/3), c(1, 0, 0)), col = "red", lty = "dotted")
TernaryText(QuartetPoints(sq_trees, cf = sq_trees$collapse_one), 1:15, 
            col = Ternary::cbPalette8[2], cex = 0.8)
TernaryText(SplitPoints(sq_trees, cf = sq_trees$collapse_one), 1:15, 
            col = Ternary::cbPalette8[3], cex = 0.8)
legend("bottomright", c("Quartets", "Splits"), bty = "n", pch = 1, cex = 0.8,
       col = Ternary::cbPalette8[2:3])