plot.phylo: Plot Phylogenies

Description

These functions plot phylogenetic trees.

Usage

# S3 method for phylo
plot(x, type = "phylogram", use.edge.length = TRUE,
     node.pos = NULL, show.tip.label = TRUE,
     show.node.label = FALSE, edge.color = NULL, edge.width
     = NULL, edge.lty = NULL, node.color = NULL, node.width
     = NULL, node.lty = NULL, 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 =
     NULL, tip.color = par("col"), plot = TRUE, rotate.tree
     = 0, open.angle = 0, node.depth = 1, align.tip.label =
     FALSE, ...)
# S3 method for 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:

type
use.edge.length
node.pos
node.depth
show.tip.label
show.node.label
font
cex
adj
srt
no.margin
label.offset
x.lim
y.lim
direction
tip.color
Ntip
Nnode
root.time
align.tip.label

Arguments

x: an object of class "phylo" or of class "multiPhylo".
type: a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial", "tidy", or any unambiguous abbreviation of these.
use.edge.length: a logical indicating whether to use the edge lengths of the phylogeny to draw the branches (the default) or not (if FALSE). This option has no effect if the object of class "phylo" has no `edge.length' element.
node.pos: a numeric taking the value 1 or 2 which specifies the vertical position of the nodes with respect to their descendants. If NULL (the default), then the value is determined in relation to `type' and `use.edge.length' (see details).
show.tip.label: a logical indicating whether to show the tip labels on the phylogeny (defaults to TRUE, i.e. the labels are shown).
show.node.label: a logical indicating whether to show the node labels on the phylogeny (defaults to FALSE, i.e. the labels are not shown).
edge.color: a vector of mode character giving the colours used to draw the branches of the plotted phylogeny. These are taken to be in the same order than the component edge of phy. If fewer colours are given than the length of edge, then the colours are recycled.
edge.width: a numeric vector giving the width of the branches of the plotted phylogeny. These are taken to be in the same order than the component edge of phy. If fewer widths are given than the length of edge, then these are recycled.
edge.lty: same as the previous argument but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash.
node.color: a vector of mode character giving the colours used to draw the perpendicular lines associated with each node of the plotted phylogeny. These are taken to be in the same order than the component node of phy. If fewer colours are given than the length of node, then the colours are recycled.
node.width: as the previous argument, but for line widths.
node.lty: as the previous argument, but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash.
font: an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).
cex: a numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters.
adj: a numeric specifying the justification of the text strings of the labels: 0 (left-justification), 0.5 (centering), or 1 (right-justification). This option has no effect if type = "unrooted". If NULL (the default) the value is set with respect of direction (see details).
srt: a numeric giving how much the labels are rotated in degrees (negative values are allowed resulting in clock-like rotation); the value has an effect respectively to the value of direction (see Examples). This option has no effect if type = "unrooted".
no.margin: a logical. If TRUE, the margins are set to zero and the plot uses all the space of the device (note that this was the behaviour of plot.phylo up to version 0.2-1 of `ape' with no way to modify it by the user, at least easily).
root.edge: a logical indicating whether to draw the root edge (defaults to FALSE); this has no effect if `use.edge.length = FALSE' or if `type = "unrooted"'.
label.offset: a numeric giving the space between the nodes and the tips of the phylogeny and their corresponding labels. This option has no effect if type = "unrooted".
underscore: a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE).
x.lim: a numeric vector of length one or two giving the limit(s) of the x-axis. If NULL, this is computed with respect to various parameters such as the string lengths of the labels and the branch lengths. If a single value is given, this is taken as the upper limit.
y.lim: same than above for the y-axis.
direction: a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards".
lab4ut: (= labels for unrooted trees) a character string specifying the display of tip labels for unrooted trees (can be abbreviated): either "horizontal" where all labels are horizontal (the default if type = "u"), or "axial" where the labels are displayed in the axis of the corresponding terminal branches. This option has an effect if type = "u", "f", or "r".
tip.color: the colours used for the tip labels, eventually recycled (see examples).
plot: a logical controlling whether to draw the tree. If FALSE, the graphical device is set as if the tree was plotted, and the coordinates are saved as well.
rotate.tree: for "fan", "unrooted", or "radial" trees: the rotation of the whole tree in degrees (negative values are accepted).
open.angle: if type = "f" or "r", the angle in degrees left blank. Use a non-zero value if you want to call axisPhylo after the tree is plotted.
node.depth: an integer value (1 or 2) used if branch lengths are not used to plot the tree; 1: the node depths are proportional to the number of tips descending from each node (the default and was the only possibility previously), 2: they are evenly spaced.
align.tip.label: a logical value or an integer. If TRUE, the tips are aligned and dotted lines are drawn between the tips of the tree and the labels. If an integer, the tips are aligned and this gives the type of the lines (lty).
layout: the number of trees to be plotted simultaneously.
...: further arguments to be passed to plot or to plot.phylo.

Author

Emmanuel Paradis, Martin Smith, Damien de Vienne

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 use align.tip.label = TRUE with type = "fan", you will have certainly to set x.lim and y.lim manually.

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

References

van der Ploeg, A. (2014) Drawing non-layered tidy trees in linear time. Journal of Software: Practice and Experience, 44, 1467--1484.

Examples

Run this code

### An extract from Sibley and Ahlquist (1990)
x <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
tree.owls <- read.tree(text= x)
plot(tree.owls)

### 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(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$edge)/2))
text(7.5, 23, "Facing trees with\ndifferent informations", font = 2)
plot(tr, "p", direction = "l", no.margin = TRUE,
     edge.width = sample(1:10, length(bird.orders$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)

## tidy trees
tr <- rtree(100)
layout(matrix(1:2, 2))
plot(tr)
axis(2)
plot(tr, "t")
axis(2)
## around 20 percent gain on the y-axis

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