plot.phylo {ape} | R Documentation |
This function plots a phylogenetic tree on the current graphical device.
plot(x, show.node.label = FALSE, edge.color = NULL, edge.width = NULL, font = 3, adj = 0, srt = 0, no.margin = FALSE, label.offset = NULL, underscore = FALSE, x.lim = NULL, ...)
x |
an object of class "phylo" . |
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. |
font |
an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic). |
adj |
a numeric specifying the justification of the text strings of the labels: 0 (left-justification, the default), 0.5 (centering), or 1 (right-justification). |
srt |
a numeric giving how much the labels are rotated in degrees (negative values are allowed resulting in clock-like rotation). |
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). |
label.offset |
a numeric giving the space between the nodes and
the tips of the phylogeny and their corresponding labels. If
NULL , this is computed with respect to various parameters
such as the string lengths of the labels. |
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 giving the limit 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. |
... |
further arguments to be passed to plot() . |
The formatting of the labels of both the nodes and the tips is the same.
The new default behaviour is to use the current margins rather
than to set them to zero. 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.
If the arguments label.offset
and x.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:'').
The function returns invisibly a list with the following components which values are those used for the current plot:
show.node.label |
|
edge.color |
|
edge.width |
|
font |
|
adj |
|
srt |
|
no.margin |
|
label.offset |
|
x.lim |
Emmanuel Paradis paradis@isem.univ-montp2.fr
read.tree
, add.scale.bar
,
plot
for the basic plotting function in R
### 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 = "\n") tree.owls <- read.tree("ex.tre") plot(tree.owls) unlink("ex.tre") # delete the file "ex.tre" data(xenarthra) op <- par() par(ask = TRUE) plot(xenarthra) ### remove the margins and put the tip labels closer ### to the tips plot(xenarthra, no.margin = TRUE, label.offset = .005) ### use a smaller font size par(cex = 0.8) plot(xenarthra, no.margin = TRUE, label.offset = .005) par(op) data(bird.orders) ### using random colours and thichness plot(bird.orders, edge.color = sample(colors(), length(bird.orders$edge)/2), edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE)) ### rainbow colouring... plot(bird.orders, edge.color = sample(c("red", "yellow", "blue", "green", "orange", "purple"), length(bird.orders$edge)/2, replace = TRUE), edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))