Plot the distribution of a character on a tree — PlotCharacter • TreeSearch

Reconstructs the distribution of a character on a tree topology using the modified Fitch algorithm presented in Brazeau et al. (2019) .

Usage

PlotCharacter(
  tree,
  dataset,
  char = 1L,
  updateTips = FALSE,
  plot = TRUE,
  tokenCol = NULL,
  ambigCol = "grey",
  inappCol = "lightgrey",
  ambigLty = "dotted",
  inappLty = "dashed",
  plainLty = par("lty"),
  tipOffset = 1,
  unitEdge = FALSE,
  ...
)

Arguments

tree: A tree of class phylo.
dataset: A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree.
char: Index of character to plot.
updateTips: Logical; if FALSE, tips will be labelled with their original state in dataset.
plot: Logical specifying whether to plot the output.
tokenCol: Palette specifying colours to associate with each token in turn, in the sequence listed in attr(dataset, "levels").
ambigCol, ambigLty, inappCol, inappLty, plainLty: Colours and line types to apply to ambiguous, inapplicable and applicable tokens. See the lty graphical parameter for details of line styles. Overrides tokenCol.
tipOffset: Numeric: how much to offset tips from their labels.
unitEdge: Logical: Should all edges be plotted with a unit length?
...: Further arguments to pass to plot.phylo().

Value

PlotCharacter() invisibly returns a matrix in which each row corresponds to a numbered tip or node of tree, and each column corresponds to a token; the tokens that might parsimoniously be present at each point on a tree are denoted with TRUE.

References

Brazeau MD, Guillerme T, Smith MR (2019). “An algorithm for morphological phylogenetic analysis with inapplicable data.” Systematic Biology, 68(4), 619–631. doi:10.1093/sysbio/syy083 .

Author

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

Examples

# Set up plotting area
oPar <- par(mar = rep(0, 4))

tree <- ape::read.tree(text = 
  "((((((a, b), c), d), e), f), (g, (h, (i, (j, (k, l))))));")
## A character with inapplicable data
dataset <- TreeTools::StringToPhyDat("23--1??--032", tips = tree)
plotted <- PlotCharacter(tree, dataset)

plotted
#>           -     0     1     2     3
#>  [1,] FALSE FALSE FALSE  TRUE FALSE
#>  [2,] FALSE FALSE FALSE FALSE  TRUE
#>  [3,]  TRUE FALSE FALSE FALSE FALSE
#>  [4,]  TRUE FALSE FALSE FALSE FALSE
#>  [5,] FALSE FALSE  TRUE FALSE FALSE
#>  [6,]  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [7,]  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [8,]  TRUE FALSE FALSE FALSE FALSE
#>  [9,]  TRUE FALSE FALSE FALSE FALSE
#> [10,] FALSE  TRUE FALSE FALSE FALSE
#> [11,] FALSE FALSE FALSE FALSE  TRUE
#> [12,] FALSE FALSE FALSE  TRUE FALSE
#> [13,]  TRUE FALSE FALSE FALSE FALSE
#> [14,]  TRUE FALSE FALSE FALSE FALSE
#> [15,]  TRUE FALSE FALSE FALSE FALSE
#> [16,]  TRUE FALSE FALSE FALSE FALSE
#> [17,]  TRUE FALSE FALSE FALSE FALSE
#> [18,] FALSE FALSE FALSE  TRUE  TRUE
#> [19,]  TRUE FALSE FALSE FALSE FALSE
#> [20,]  TRUE FALSE FALSE FALSE FALSE
#> [21,]  TRUE FALSE FALSE FALSE FALSE
#> [22,] FALSE  TRUE FALSE  TRUE  TRUE
#> [23,] FALSE  TRUE FALSE  TRUE  TRUE

# Character from a real dataset 
data("Lobo", package = "TreeTools")
dataset <- Lobo.phy
tree <- TreeTools::NJTree(dataset)
PlotCharacter(tree, dataset, 14)

par(oPar)