nodelabels {ape} | R Documentation |
This function adds labels to or near the nodes of a tree using text or plotting symbols. The text can be framed.
nodelabels(text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, thermo = NULL, col = "black", bg = "lightblue", ...)
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 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 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). |
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.
Emmanuel Paradis paradis@isem.univ-montp2.fr
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")