R: Visualize position of rogue taxa

RoguePlot {TreeTools}

R Documentation

Visualize position of rogue taxa

Description

Plots a consensus of trees with a rogue taxon omitted, with edges coloured according to the proportion of trees in which the taxon attaches to that edge, after Klopfstein and Spasojevic (2019).

Usage

RoguePlot(
  trees,
  tip,
  p = 1,
  plot = TRUE,
  Palette = colorRampPalette(c(par("fg"), "#009E73"), space = "Lab"),
  nullCol = rgb(colorRamp(unlist(par(c("fg", "bg"))), space = "Lab")(0.8)/255),
  edgeLength = NULL,
  thin = par("lwd"),
  fat = thin + 1L,
  outgroupTips,
  ...
)

Arguments

`trees`	List or `multiPhylo` object containing phylogenetic trees of class `phylo` to be summarized.
`tip`	Numeric or character identifying rogue leaf, in format accepted by `DropTip()`.
`p`	A numeric value between 0.5 and 1 giving the proportion for a clade to be represented in the consensus tree (see `Consensus()`).
`plot`	Logical specifying whether to plot the tree.
`Palette`	Function that takes a parameter `n` and generates a colour palette with `n` entries.
`nullCol`	Colour to paint regions of the tree on which the rogue is never found.
`edgeLength`	Numeric specifying edge lengths of consensus tree; `NULL` aligns tips by scaling edges proportional to clade size; `1` sets all edges to unit length.
`thin, fat`	Numeric specifying width to plot edges if the rogue tip never / sometimes does attach to them.
`outgroupTips`	Vector of type character, integer or logical, specifying the names or indices of the tips to include in the outgroup. If `outgroupTips` is a of type character, and a tree contains multiple tips with a matching label, the first will be used.
`...`	Additional parameters to `plot.phylo()`.

Details

Rogue taxa can be identified using the package Rogue (Smith 2022).

Value

RoguePlot() returns a list whose elements are:

cons: The reduced consensus tree, in preorder;
onEdge: a vector of integers specifying the number of trees in trees in which the rogue leaf is attached to each edge in turn of the consensus tree;
atNode: a vector of integers specifying the number of trees in trees in which the rogue leaf is attached to an edge collapsed into each node of the consensus tree.

Author(s)

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

References

Klopfstein S, Spasojevic T (2019). “Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix.” PLOS ONE, 14(4), e0212942. doi: 10.1371/journal.pone.0212942.

Smith MR (2022). “Using information theory to detect rogue taxa and improve consensus trees.” Systematic Biology, Online ahead of print, syab099. doi: 10.1093/sysbio/syab099.

Examples

trees <- list(read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"),
              read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"),
              read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"),
              read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"),
              read.tree(text = "(rogue, (a, (b, (c, (d, (e, f))))));"),
              read.tree(text = "((rogue, a), (b, (c, (d, (e, f)))));"),
              read.tree(text = "(a, (b, ((c, d), (rogue, (e, f)))));"),
              read.tree(text = "(a, (b, ((c, (rogue, d)), (e, f))));"),
              read.tree(text = "(a, (b, (c, (d, (rogue, (e, f))))));"))
RoguePlot(trees, "rogue")

[Package TreeTools version 1.7.2 Index]