ade4: newick2phylog – R documentation

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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)

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

Value

Return object of class phylog.

Author(s)

Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr

Examples

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

## Not run: 
# 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)

## End(Not run)

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release