ape (version 1.7)

nodelabels: Labelling the Nodes of a Tree

Description

This function adds labels to or near the nodes 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, col = "black",
           bg = "lightblue", ...)

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.

adj

one or two numeric values specifying the horizontal and vertical, respectively, justification of the text. By default, the text is centered horizontally and vertically. If a single value is given, this alters only the horizontal position of th

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 for each node (the thermometers are filled up to this level), or a two-column matrix giving two proportions (the thermometers are filled between these two levels).

col

a character string giving the color to be used for 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).

Details

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

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

A simple call of the function with no arguments (i.e. nodelabels()) prints the numbers of all nodes.

See Also

plot.phylo

Examples

tr <- read.tree(text = "((Homo,Pan),Gorilla);")
plot(tr)
nodelabels("7.3 Ma", 1, frame = "r", bg = "yellow", adj = 0)
nodelabels("5.4 Ma", 2, frame = "c", bg = "tomato", font = 3)

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")