newick2phylog {ade4} | R Documentation |
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 |
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 |
Value
Return object of class phylog
.
Author(s)
Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr
See Also
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)