Visualize position of rogue taxa

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,
  sort = FALSE,
  legend = "none",
  legend.inset = 0,
  ...
)

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.
sort: Logical specifying whether to sort consensus tree using SortTree().
legend: Character vector specifying position of legend (e.g. "bottomleft"), or "none" to suppress legend. For fine-grained control of legend, use PlotTools::SpectrumLegend().
legend.inset: Numeric specifying fraction of plot width / height by which the legend's position should be inset.
...: Additional parameters to plot.phylo().

Value

RoguePlot() invisibly 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.
legendLabels: A character vector suggesting labels for a plot legend; suitable for PlotTools::SpectrumLegend(legend = x$legendLabels).

Details

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

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, 71(5), 986–1008. doi:10.1093/sysbio/syab099 .

Author

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

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))))));"))
plotted <- RoguePlot(trees, "rogue", legend = "topleft", legend.inset = 0.02)
PlotTools::SpectrumLegend(
  "bottomleft",
  palette = colorRampPalette(c(par("fg"), "#009E73"), space = "Lab")(100),
  legend = plotted$legendLabels,
  cex = 0.4
)