ape (version 1.8-4)

nodelabels: Labelling the Nodes and the Tips of a Tree

Description

These functions add labels to or near the nodes or the tips 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", ...)
tiplabels(text, tip, adj = c(0.5, 0.5), frame = "rect",
          pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
          col = "black", bg = "yellow", ...)

Details

These two 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 (or tip) is missing, then the text or the symbols are printed on all nodes (or tips).

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 will 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).

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")

### 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)
### Some random data to compare piecharts and thermometres:
tr <- rcoal(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)
layout(matrix(1))

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