Skip to contents

Plot concordance table

Source: R/Concordance.R
ConcordanceTable.Rd

ConcordanceTable() plots a concordance table (Smith 2026) .

Usage

ConcordanceTable(
  tree,
  dataset,
  Col = QACol,
  largeClade = 0,
  xlab = "Edge",
  ylab = "Character",
  ...
)

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. Perhaps load into R using ReadAsPhyDat(). Additive (ordered) characters can be handled using Decompose().

Col

Function that takes vectors amount and quality and returns a vector of colours. QCol colours by data quality (concordance); QACol by quality and amount of information.

largeClade

Integer; if greater than 1, vertical lines will be drawn at edges whose descendants are both contain more than largeClade leaves.

xlab

Character giving a label for the x axis.

ylab

Character giving a label for the y axis.

...

Arguments to abline, to control the appearance of vertical lines marking important edges.

Value

ConcordanceTable() invisibly returns an named list containing:

  • "info": The amount of information in each character-edge pair, in bits;

  • "relInfo": The information, normalized to the most information-rich pair;

  • "quality": The normalized mutual information of the pair;

  • "col": The colours used to plot the table.

References

Smith MR (2026). “Which characters support which clades? Exploring the distribution of phylogenetic signal using concordant information.” Forthcoming.

See also

Other split support functions: JackLabels(), Jackknife(), MaximizeParsimony(), MostContradictedFreq(), PresCont(), SiteConcordance

Examples

# Load data and tree
data("congreveLamsdellMatrices", package = "TreeSearch")
dataset <- congreveLamsdellMatrices[[1]][, 1:20]
tree <- referenceTree

# Plot tree and identify nodes
library("TreeTools", quietly = TRUE)
plot(tree)
nodeIndex <- as.integer(rownames(as.Splits(tree)))
nodelabels(seq_along(nodeIndex), nodeIndex, adj = c(2, 1),
           frame = "none", bg = NULL)
QALegend(where = c(0.1, 0.4, 0.1, 0.3))


# View information shared by characters and edges
ConcordanceTable(tree, dataset, largeClade = 3, col = 2, lwd = 3)
axis(1)
axis(2)


# Visualize dataset
image(t(`mode<-`(PhyDatToMatrix(dataset), "numeric")), axes = FALSE,
      xlab = "Leaf", ylab = "Character")