| plot.phylog {ade4} | R Documentation |
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.
## 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)
x, phylog |
an object of class |
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 |
cnodes |
a character size for plotting the points that represent the nodes, used with |
labels.leaves |
a vector of strings of characters for the leaves labels |
clabel.leaves |
a character size for the leaves labels, used with |
labels.nodes |
a vector of strings of characters for the nodes labels |
clabel.nodes |
a character size for the nodes labels, used with |
sub |
a string of characters to be inserted as legend |
csub |
a character size for the legend, used with |
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 |
... |
further arguments passed to or from other methods |
no.over |
a size coefficient for the number of representations |
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.
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.
Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr
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)