plot.phylog: Plot phylogenies

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Plot phylogenies

Description

plot.phylog draws phylogenetic trees as linear dendograms.
radial.phylog draws phylogenetic trees as circular dendograms.
enum.phylog enumerate all the possible representations for a phylogeny.

Usage

## S3 method for class 'phylog'
plot(x, y = NULL, f.phylog = 0.5, cleaves = 1, cnodes = 0,
 labels.leaves = names(x$leaves), clabel.leaves = 1,
 labels.nodes = names(x$nodes), clabel.nodes = 0, sub = "",
 csub = 1.25, possub = "bottomleft", draw.box = FALSE, ...)
radial.phylog(phylog, circle = 1, cleaves = 1, cnodes = 0,
 labels.leaves = names(phylog$leaves), clabel.leaves = 1,
 labels.nodes = names(phylog$nodes), clabel.nodes = 0,
 draw.box = FALSE)
enum.phylog(phylog, no.over = 1000)

Arguments

x, phylog	an object of class phylog
y	a vector which values correspond to leaves positions
f.phylog	a size coefficient for tree size (a parameter to draw the tree in proportion to leaves label)
circle	a size coefficient for the outer circle
cleaves	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
cnodes	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
labels.leaves	a vector of strings of characters for the leaves labels
clabel.leaves	a character size for the leaves labels, used with par("cex")*clabel.leaves. If zero, no leaves labels are drawn
labels.nodes	a vector of strings of characters for the nodes labels
clabel.nodes	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
sub	a string of characters to be inserted as legend
csub	a character size for the legend, used with par("cex")*csub
possub	a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright")
draw.box	if TRUE draws a box around the current plot with the function box()
...	further arguments passed to or from other methods
no.over	a size coefficient for the number of representations

Details

The vector y is an argument of the function plot.phylog that ensures to plot one of the possible representations of a phylogeny. The vector y is a permutation of the set of leaves {1,2,...,f} compatible with the phylogeny's topology.

Value

The function enum.phylog returns a matrix with as many columns as leaves. Each row gives a permutation of the set of leaves {1,2,...,f} compatible with the phylogeny's topology.

Author(s)

Daniel Chessel
Sébastien Ollier [e-mail]

See Also

phylog

Examples

data(newick.eg)
par(mfrow = c(3,2))
for(i in 1:6) plot(newick2phylog(newick.eg[[i]], FALSE),
 clea = 2, clabel.l = 3, cnod = 2.5)
par(mfrow = c(1,1))

## Not run: 
par(mfrow = c(1,2))
plot(newick2phylog(newick.eg[[11]], FALSE), clea = 1.5,
 clabel.l = 1.5, clabel.nod = 0.75, f = 0.8)
plot(newick2phylog(newick.eg[[10]], FALSE), clabel.l = 0,
 clea = 0, cn = 0, f = 1)
par(mfrow = c(1,1))

## End(Not run)

par(mfrow = c(2,2))
w7 <- newick2phylog("(((((1,2,3)b),(6)c),(4,5)d,7)f);")
plot(w7,clabel.l = 1.5, clabel.n = 1.5, f = 0.8, cle = 2,
 cnod = 3, sub = "(((((1,2,3)b),(6)c),(4,5)d,7)f);", csub = 2)
w <- NULL
w[1] <- "((((e1:4,e2:4)a:5,(e3:7,e4:7)b:2)c:2,e5:11)d:2,"
w[2] <- "((e6:5,e7:5)e:4,(e8:4,e9:4)f:5)g:4);"
plot(newick2phylog(w), f = 0.8, cnod = 2, cleav = 2, clabel.l = 2)

data(taxo.eg)
w <- taxo2phylog(as.taxo(taxo.eg[[1]]))
plot(w, clabel.lea = 1.25, clabel.n = 1.25, sub = "Taxonomy",
 csub = 3, f = 0.8, possub = "topleft")

provi.tre <- "(((a,b,c,d,e)A,(f,g,h)B)C)D;"
provi.phy <- newick2phylog(provi.tre)
plot(provi.phy, clabel.l = 2, clabel.n = 2, f = 0.8)
par(mfrow = c(1,1))

## Not run: 
par(mfrow = c(3,3))
for (j in 1:6) radial.phylog(newick2phylog(newick.eg[[j]],
 FALSE), clabel.l = 2, cnodes = 2)
radial.phylog(newick2phylog(newick.eg[[7]],FALSE), clabel.l = 2)
radial.phylog(newick2phylog(newick.eg[[8]],FALSE), clabel.l = 0,
 circle = 1.8)
radial.phylog(newick2phylog(newick.eg[[9]],FALSE), clabel.l = 1,
 clabel.n = 1, cle = 0, cnode = 1)
par(mfrow = c(1,1))

data(bsetal97)
bsetal.phy = taxo2phylog(as.taxo(bsetal97$taxo[,1:3]), FALSE)
radial.phylog(bsetal.phy, cnod = 1, clea = 1, clabel.l = 0.75,
 draw.box = TRUE, cir = 1.1)
par(mfrow = c(1,1))

## End(Not run)

## Not run: 
# plot all the possible representations of a phylogenetic tree
a <- "((a,b)A,(c,d,(e,f)B)C)D;"
wa <- newick2phylog(a)
wx <- enum.phylog(wa)
dim(wx)

par(mfrow = c(6,8))
fun <- function(x) {
    w  <-NULL
    lapply(x, function(y) w<<-paste(w,as.character(y),sep=""))
    plot(wa, x, clabel.n = 1.25, f = 0.75, clabel.l = 2,
     box = FALSE, cle = 1.5, sub = w, csub = 2)
    invisible()}
apply(wx,1,fun)
par(mfrow = c(1,1))

## End(Not run)

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.