ape (version 2.2-3)

plot.phylo: Plot Phylogenies

Description

These functions plot phylogenetic trees on the current graphical device.

Usage

## S3 method for class 'phylo':
plot(x, type = "phylogram", use.edge.length = TRUE,
    node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE,
    edge.color = "black", edge.width = 1, font = 3,
    cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
    root.edge = FALSE, label.offset = 0, underscore = FALSE,
    x.lim = NULL, y.lim = NULL, direction = "rightwards",
    lab4ut = "horizontal", tip.color = "black", ...)
## S3 method for class 'multiPhylo':
plot(x, layout = 1, ...)

Value

plot.phylo returns invisibly a list with the following components which values are those used for the current plot:typeuse.edge.lengthnode.posshow.tip.labelshow.node.labelfontcexadjsrtno.marginlabel.offsetx.limy.limdirectiontip.colorNtipNnode

Details

If x is a list of trees (i.e., an object of class "multiPhylo"), then any further argument may be passed with ... and could be any one of those listed above for a single tree.

The font format of the labels of the nodes and the tips is the same.

If no.margin = TRUE, the margins are set to zero and are not restored after plotting the tree, so that the user can access the coordinates system of the plot.

The option `node.pos' allows the user to alter the vertical position (i.e. ordinates) of the nodes. If node.pos = 1, then the ordinate of a node is the mean of the ordinates of its direct descendants (nodes and/or tips). If node.pos = 2, then the ordinate of a node is the mean of the ordinates of all the tips of which it is the ancestor. If node.pos = NULL (the default), then its value is determined with respect to other options: if type = "phylogram" then `node.pos = 1'; if type = "cladogram" and use.edge.length = FALSE then `node.pos = 2'; if type = "cladogram" and use.edge.length = TRUE then `node.pos = 1'. Remember that in this last situation, the branch lengths make sense when projected on the x-axis.

If adj is not specified, then the value is determined with respect to direction: if direction = "leftwards" then adj = 1 (0 otherwise).

If the arguments x.lim and y.lim are not specified by the user, they are determined roughly by the function. This may not always give a nice result: the user may check these values with the (invisibly) returned list (see ``Value:'').

If you resize manually the graphical device (windows or X11) you may need to replot the tree.

See Also

read.tree, add.scale.bar, axisPhylo, nodelabels, plot for the basic plotting function in R

Examples

### An extract from Sibley and Ahlquist (1990)
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
   "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
   file = "ex.tre", sep = "")
tree.owls <- read.tree("ex.tre")
plot(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"

### Show the types of trees.
layout(matrix(1:6, 3, 2))
plot(tree.owls, main = "With branch lengths")
plot(tree.owls, type = "c")
plot(tree.owls, type = "u")
plot(tree.owls, use.edge.length = FALSE, main = "Without branch lengths")
plot(tree.owls, type = "c", use.edge.length = FALSE)
plot(tree.owls, type = "u", use.edge.length = FALSE)
layout(matrix(1))

data(xenarthra)
plot(xenarthra)
### remove the margins...
plot(xenarthra, no.margin = TRUE)
### ... and use a smaller font size
plot(xenarthra, no.margin = TRUE, cex = 0.8)
plot(xenarthra, type = "c", no.margin = TRUE,
     use.edge.length = FALSE, cex = 0.8)
par(mar = c(5.1, 4.1, 4.1, 2.1))

data(bird.orders)
### using random colours and thickness
plot(bird.orders,
     edge.color = sample(colors(), length(bird.orders$edge)/2),
     edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Random colours and branch thickness")
### rainbow colouring...
X <- c("red", "orange", "yellow", "green", "blue", "purple")
plot(bird.orders,
     edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
     edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Rainbow colouring")
plot(bird.orders, type = "c", use.edge.length = FALSE,
     edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
     edge.width = rep(5, length(bird.orders$edge)/2))
segments(rep(0, 6), 6.5:1.5, rep(2, 6), 6.5:1.5, lwd = 5, col = X)
text(rep(2.5, 6), 6.5:1.5, paste(X, "..."), adj = 0)
title("Character mapping...")
plot(bird.orders, "u", font = 1, cex = 0.75)
data(bird.families)
plot(bird.families, "u", lab4ut = "axial", font = 1, cex = 0.5)
plot(bird.families, "r", font = 1, cex = 0.5)
### cladogram with oblique tip labels
plot(bird.orders, "c", FALSE, direction = "u", srt = -40, x.lim = 25.5)
### facing trees with different informations...
tr <- bird.orders
tr$tip.label <- rep("", 23)
layout(matrix(1:2, 1, 2), c(5, 4))
plot(bird.orders, "c", FALSE, adj = 0.5, no.margin = TRUE, label.offset = 0.8,
     edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
     edge.width = rep(5, length(bird.orders$edge)/2))
text(7.5, 23, "Facing trees with
different informations", font = 2)
plot(tr, "p", direction = "l", no.margin = TRUE,
     edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
### Recycling of arguments gives a lot of possibilities
### for tip labels:
plot(bird.orders, tip.col = c(rep("red", 5), rep("blue", 18)),
     font = c(rep(3, 5), rep(2, 17), 1))
plot(bird.orders, tip.col = c("blue", "green"),
     cex = 23:1/23 + .3, font = 1:3)
co <- c(rep("blue", 9), rep("green", 35))
plot(bird.orders, "f", edge.col = co)
plot(bird.orders, edge.col = co)
layout(1)