ape (version 3.3)

phydataplot: Tree Annotation

Description

phydataplot plots data on a tree in a way that adapts to the type of tree. ring does the same for circular trees.

Both functions match the data with the labels of the tree.

Usage

phydataplot(x, phy, style = "bars", offset = 1, ...)
ring(x, phy, style = "ring", offset = 1, ...)

Arguments

x

a vector, a factor, a matrix, or a data frame.

phy

the tree (which must be already plotted).

style

a character string specifying the type of graphics; can be abbreviated (see details).

offset

the space between the tips of the tree and the plot.

...

further arguments passed to the graphical functions.

Details

The possible values for style are ``bars'', ``segments'', ``image'', or ``arrows'' for phydataplot, and ``ring'', ``segments'', or ``arrows'' for ring.

See Also

plot.phylo, nodelabels, fancyarrows

Examples

## demonstrates matching with names:
tr <- rcoal(n <- 10)
x <- 1:n
names(x) <- tr$tip.label
plot(tr, x.lim = 11)
phydataplot(x, tr)
## shuffle x but matching names with tip labels reorders them:
phydataplot(sample(x), tr, "s", lwd = 3, lty = 3)

## adapts to the tree:
plot(tr, "f", x.l = c(-11, 11), y.l = c(-11, 11))
phydataplot(x, tr, "s")

## leave more space with x.lim to show 2 barplots:
plot(tr, x.lim = 22)
phydataplot(x, tr, "b")
phydataplot(x, tr, "b", offset = 12, col = "yellow")

ts <- rcoal(N <- 100)
X <- rTraitCont(ts) # names are set
dd <- dist(X)
op <- par(mar = rep(0, 4))
plot(ts, x.lim = 10, cex = 0.4, font = 1)
phydataplot(as.matrix(dd), ts, "i", offset = 0.2)

par(xpd = TRUE, mar = op$mar)
co <- c("blue", "red"); l <- c(-2, 2)
X <- X + abs(min(X)) # move scale so X >= 0
plot(ts, "f", show.tip.label = FALSE, x.lim = l, y.lim = l, open.angle = 30)
phydataplot(X, ts, "s", col = co, offset = 0.05)
ring(X, ts, "ring", col = co, offset = max(X) + 0.1) # the same info as a ring

## as many rings as you want...
co <- c("blue", "yellow")
plot(ts, "r", show.tip.label = FALSE, x.l = c(-1, 1), y.l = c(-1, 1))
for (o in seq(0, 0.4, 0.2)) {
    co <- rev(co)
    ring(0.2, ts, "r", col = rep(co, each = 5), offset = o)
}

lim <- c(-5, 5)
co <- rgb(0, 0.4, 1, alpha = 0.1)
y <- seq(0.01, 1, 0.01)
plot(ts, "f", x.lim = lim, y.lim = lim, show.tip.label = FALSE)
ring(y, ts, offset = 0, col = co, lwd = 0.1)
for (i in 1:3) {
    y <- y + 1
    ring(y, ts, offset = 0, col = co, lwd = 0.1)
}

## rings can be in the background
plot(ts, "r", plot = FALSE)
ring(1, ts, "r", col = rainbow(100), offset = -1)
par(new = TRUE)
plot(ts, "r", font = 1, edge.color = "white")

## might be more useful:
co <- c("lightblue", "yellow")
plot(ts, "r", plot = FALSE)
ring(0.1, ts, "r", col = sample(co, size = N, rep = TRUE), offset = -.1)
par(new = TRUE)
plot(ts, "r", font = 1)

## if x is matrix:
tx <- rcoal(m <- 20)
X <- runif(m, 0, 0.5); Y <- runif(m, 0, 0.5)
X <- cbind(X, Y, 1 - X - Y)
rownames(X) <- tx$tip.label
plot(tx, x.lim = 6)
co <- rgb(diag(3))
phydataplot(X, tx, col = co)
## a variation:
plot(tx, show.tip.label = FALSE, x.lim = 5)
phydataplot(X, tx, col = co, offset = 0.05, border = NA)

plot(tx, "f", show.tip.label = FALSE, open.angle = 180)
ring(X, tx, col = co, offset = 0.05)

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