newick2phylog {ade4} | R Documentation |
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.
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)
x.tre |
a character string corresponding to a phylogenetic tree in Newick format |
add.tools |
if TRUE, executes the function |
call |
call |
hc |
an object of class |
taxo |
an object of class |
res |
an object of class |
tol |
used in case 3 of |
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 |
Return object of class phylog
.
Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr
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)