nodelabels: Labelling the Nodes, Tips, and Edges of a Tree

Description

These functions add labels to or near the nodes, the tips, or the edges of a tree using text or plotting symbols. The text can be framed.

Usage

nodelabels(text, node, adj = c(0.5, 0.5), frame = "rect",
           pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
           col = "black", bg = "lightblue", horiz = FALSE,
           width = NULL, height = NULL, ...)
tiplabels(text, tip, adj = c(0.5, 0.5), frame = "rect",
          pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
          col = "black", bg = "yellow", horiz = FALSE,
          width = NULL, height = NULL, offset = 0, ...)
edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
           pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
           col = "black", bg = "lightgreen", horiz = FALSE,
           width = NULL, height = NULL, date = NULL, ...)

Arguments

text: a vector of mode character giving the text to be printed. Can be left empty.
node: a vector of mode numeric giving the numbers of the nodes where the text or the symbols are to be printed. Can be left empty.
tip: a vector of mode numeric giving the numbers of the tips where the text or the symbols are to be printed. Can be left empty.
edge: a vector of mode numeric giving the numbers of the edges where the text or the symbols are to be printed. Can be left empty.
adj: one or two numeric values specifying the horizontal and vertical, respectively, justification of the text or symbols. By default, the text is centered horizontally and vertically. If a single value is given, this alters only the horizontal position of the text.
frame: a character string specifying the kind of frame to be printed around the text. This must be one of "rect" (the default), "circle", "none", or any unambiguous abbreviation of these.
pch: a numeric giving the type of plotting symbol to be used; this is eventually recycled. See par for R's plotting symbols. If pch is used, then text is ignored.
thermo: a numeric vector giving some proportions (values between 0 and 1) for each node, or a numeric matrix giving some proportions (the rows must sum to one). It can be a data frame which is then converted into a matrix.
pie: same than thermo.
piecol: a list of colours (given as a character vector) to be used by thermo or pie; if left NULL, a series of colours given by the function rainbow is used.
col: a character string giving the color to be used for the text or the plotting symbols; this is eventually recycled.
bg: a character string giving the color to be used for the background of the text frames or of the plotting symbols if it applies; this is eventually recycled.
...: further arguments passed to the text or points functions (e.g. cex to alter the size of the text or the symbols, or font for the text; see the examples below).
horiz, width, height: parameters controlling the aspect of thermometers; by default, their width and height are determined automatically.
offset: offset of the tip labels (can be negative).
date: specifies the positions of labels on edges of chronograms with respect to the time scale.

Author

Emmanuel Paradis, Ben Bolker, and Jim Lemon

Details

These three functions have the same optional arguments and the same functioning.

If the arguments text is missing and pch and thermo are left as NULL, then the numbers of the nodes (or of the tips) are printed.

If node, tip, or edge is missing, then the text or the symbols are printed on all nodes, tips, or edges.

The option cex can be used to change the size of all types of labels.

A simple call of these functions with no arguments (e.g., nodelabels()) prints the numbers of all nodes (or tips).

In the case of tiplabels, it would be useful to play with the options x.lim and label.offset (and possibly show.tip.label) of plot.phylo in most cases (see the examples).

Examples

Run this code

tr <- read.tree(text = "((Homo,Pan),Gorilla);")
plot(tr)
nodelabels("7.3 Ma", 4, frame = "r", bg = "yellow", adj = 0)
nodelabels("5.4 Ma", 5, frame = "c", bg = "tomato", font = 3)

## A trick by Liam Revell when there are many categories:
plot(tr, x.lim = c(-1, 4))
nodelabels(node = 4, pie = matrix(rep(1, 100), 1), cex = 5)
op <- par(fg = "transparent")
nodelabels(node = 5, pie = matrix(rep(1, 100), 1), cex = 5)
par(op)

data(bird.orders)
plot(bird.orders, use.edge.length = FALSE, font = 1)
bs <- round(runif(22, 90, 100), 0) # some imaginary bootstrap values
bs2 <- round(runif(22, 90, 100), 0)
bs3 <- round(runif(22, 90, 100), 0)
nodelabels(bs, adj = 1.2)
nodelabels(bs2, adj = -0.2, bg = "yellow")

### something more classical
plot(bird.orders, use.edge.length = FALSE, font = 1)
nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8)
nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8)
nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)

### the same but we play with the font
plot(bird.orders, use.edge.length = FALSE, font = 1)
nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8, font = 2)
nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8, font = 3)
nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)

plot(bird.orders, "c", use.edge.length = FALSE, font = 1)
nodelabels(thermo = runif(22), cex = .8)

plot(bird.orders, "u", FALSE, font = 1, lab4ut = "a")
nodelabels(cex = .75, bg = "yellow")

### representing two characters at the tips (you could have as many
### as you want)
plot(bird.orders, "c", FALSE, font = 1, label.offset = 3,
     x.lim = 31, no.margin = TRUE)
tiplabels(pch = 21, bg = gray(1:23/23), cex = 2, adj = 1.4)
tiplabels(pch = 19, col = c("yellow", "red", "blue"), adj = 2.5, cex = 2)
### This can be used to highlight tip labels:
plot(bird.orders, font = 1)
i <- c(1, 7, 18)
tiplabels(bird.orders$tip.label[i], i, adj = 0)
### Some random data to compare piecharts and thermometres:
tr <- rtree(15)
x <- runif(14, 0, 0.33)
y <- runif(14, 0, 0.33)
z <- runif(14, 0, 0.33)
x <- cbind(x, y, z, 1 - x - y - z)
layout(matrix(1:2, 1, 2))
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(pie = x, cex = 1.3)
text(4.5, 15, "Are you \"pie\"...", font = 4, cex = 1.5)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
text(4.5, 15, "... or \"thermo\"?", font = 4, cex = 1.5)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), width = 3, horiz = TRUE)
layout(1)
plot(tr, main = "Showing Edge Lengths")
edgelabels(round(tr$edge.length, 3), srt = 90)
plot(tr, "p", FALSE)
edgelabels("above", adj = c(0.5, -0.25), bg = "yellow")
edgelabels("below", adj = c(0.5, 1.25), bg = "lightblue")