plot.phylog: Plot phylogenies

Description Usage Arguments Details Value Author(s) See Also Examples

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

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## 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 sebastien.ollier@u-psud.fr

See Also

phylog

Examples

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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 May 2, 2019, 5:50 p.m.

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