Plot the distribution of a character on a tree

Reconstructs the distribution of a character on a tree topology using the modified Fitch algorithm presented in Brazeau2019;textualTreeSearch.

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,
  Display = function(tree) tree,
  ...
)

# S3 method for class 'phylo'
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,
  Display = function(tree) tree,
  ...
)

# S3 method for class 'multiPhylo'
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,
  Display = function(tree) tree,
  ...
)

# S3 method for class 'list'
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,
  Display = function(tree) tree,
  ...
)

Arguments

tree

A bifurcating tree of class phylo, or a list or multiPhylo object containing such trees.

dataset

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree. Perhaps load into R using ReadCharacters.

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?

Display

Function that takes argument tree and returns a tree of class phylo, formatted as it will be plotted.

...

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. If multiple trees are supplied, the strict consensus of all trees and reconstructions will be returned; i.e. if a node is reconstructed as $0$ in one tree, and $2$ in another, it will be labelled $(02)$.

References

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)