ade4 (version 1.7-22)

newick2phylog: Create phylogeny

Description

The first three functions ensure to create object of class phylog from either a character string in Newick format (newick2phylog) or an object of class 'hclust' (hclust2phylog) or a taxonomy (taxo2phylog). The function newick2phylog.addtools is an internal function called by newick2phylog, hclust2phylog and taxo2phylog when newick2phylog.addtools = TRUE. It adds some items in 'phylog' objects.

Usage

newick2phylog(x.tre, add.tools = TRUE, call = match.call())
hclust2phylog(hc, add.tools = TRUE)
taxo2phylog(taxo, add.tools = FALSE, root="Root", abbrev=TRUE)
newick2phylog.addtools(res, tol = 1e-07)

Value

Return object of class phylog.

Arguments

x.tre

a character string corresponding to a phylogenetic tree in Newick format
(http://evolution.genetics.washington.edu/phylip/newicktree.html)

add.tools

if TRUE, executes the function newick2phylog.addtools

call

call

hc

an object of class hclust

taxo

an object of class taxo

res

an object of class phylog (an internal argument of the function newick2phylog)

tol

used in case 3 of method as a tolerance threshold for null eigenvalues

root

a character string for the root of the tree

abbrev

logical : if TRUE levels are abbreviated by column and two characters are added before

Author

Daniel Chessel
Sébastien Ollier

See Also

phylog, plot.phylog, as.taxo

Examples

 w <- "((((,,),,(,)),),(,));"
 w.phy <- newick2phylog(w)
 print(w.phy)
 plot(w.phy)

if (FALSE) {
# newick2phylog
data(newick.eg)
radial.phylog(newick2phylog(newick.eg[[8]], FALSE), cnode = 1,
 clabel.l = 0.8)

w <- NULL
w[1] <- "(,((((((((((((((((,,(,(,))),),(((,(,)),(,)),),(,(,)),(,)),((((("
w[2] <- ",(,)),),),(,)),((((,((,),((,(,)),))),(,)),(,(,),,((,),(,)),)),("
w[3] <- "(((((,),),(,(,))),),(,)),(((,),),)))),((,,((,),)),(,)),((,),(,)"
w[4] <- ")),(((((((((,,),),,),),((,),)),(,),((,),)),),(((((,),),),((,),)"
w[5] <- "),(((,(,(,(,)))),(,)),(((,),(((((((,),),),,),(,)),(,)),)),((,)"
w[6] <- ",))))),(,((,),(,)),((,(,)),)))),((((,(,(,))),((,(,)),,((,(,)),)"
w[7] <- ",)),(((,),),(((,),),))),((,),))),((((((((((,,,,(,)),),((,),)),("
w[8] <- ",(,))),(((((((((,(,)),(,)),((((,((,),(,(,(,))))),((,),(,(,)))),"
w[9] <- "),((,),))),(((((((((,(,)),((,),(,))),),),),(((,((,),)),),((,((,"
w[10] <- "),)),)),(,)),(,(,(,)))),((((,(,)),(,)),(((,),(,)),(,),,(,))),(,"
w[11] <- "))),(,,,))),((((,),),),(((,(,(,))),((,),)),(,)))),(,)),),(,((,("
w[12] <- ",)),),(((,),),))),),(((,),),(,),(,(,))),(((,),(,)),((,),(,)))),"
w[13] <- "(((,),((,),)),(((((,,,,,),(,)),(,)),(,((,),))),))),(,(((((,(((("
w[14] <- ",(,)),),),)),),((,((,),((,((,),(,))),))),)),((((,),(((,),(,(,))"
w[15] <- "),)),),)),((,),)))),(((,((,,((,),)),)),),((,),))),((,),(,))),(("
w[16] <- ",),)),(((((,),((,(,)),(((,(,)),(,(((,),),))),))),(,),,),),),,(,"
w[17] <- ")),((((,),,),),((,,,),((,),((,),))))),((((((,(,)),,(,)),,(,),(,"
w[18] <- "),),(((((,(,(,),)),(((,),,),(,))),),),),,,((,),)),),)),(((((,),"
w[19] <- "(,(,)),),((,((,),),,),)),(((((((,),((((,,,),(,(,))),(((,(,)),),"
w[20] <- "(,))),)),),),),(,)),),),((,),))),((,),)),(((((((((((,),),(((((("
w[21] <- ",),),((,),)),(,)),),)),(,)),),((((((,),),(((,),),)),(,)),),(,))"
w[22] <- ",),),),),(,)),),((,),(,),,,)),(,(,(,)))),),(,)),),);"
phy1 <- newick2phylog(w,FALSE)
phy1
radial.phylog(phy1, clabel.l = 0, circle = 2.2, clea = 0.5,
 cnod = 0.5)
data(newick.eg)
radial.phylog(newick2phylog(newick.eg[[8]], FALSE), cnode = 1,
 clabel.l = 0.8)

# hclust2phylog
data(USArrests)
hc <- hclust(dist(USArrests), "ave")
par(mfrow = c(1,2))
plot(hc, hang = -1)
phy <- hclust2phylog(hc)
plot(phy, clabel.l = 0.75, clabel.n = 0.6, f = 0.75)

par(mfrow = c(1,1))
row.names(USArrests) 
names(phy$leaves) #WARNING not the same for two reasons
row.names(USArrests) <- gsub(" ","_",row.names(USArrests))
row.names(USArrests) 
names(phy$leaves) #WARNING not the same for one reason
USArrests <- USArrests[names(phy$leaves),]
row.names(USArrests) 
names(phy$leaves) #the same
table.phylog(data.frame(scalewt(USArrests)), phy, csi = 2.5,
 clabel.r = 0.75, f = 0.7)

#taxo2phylog
data(taxo.eg)
tax <- as.taxo(taxo.eg[[1]])
tax.phy <- taxo2phylog(as.taxo(taxo.eg[[1]]))
par(mfrow = c(1,2))
plot(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
plot(taxo2phylog(as.taxo(taxo.eg[[1]][sample(15),])),
 clabel.l = 1.25, clabel.n = 1.25, f = 0.75)

par(mfrow=c(1,1))
plot(taxo2phylog(as.taxo(taxo.eg[[2]])), clabel.l = 1,
 clabel.n = 0.75, f = 0.65)
}