| 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 (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 |
Return object of class phylog.
Daniel Chessel
Sébastien Ollier ollier@biomserv.univ-lyon1.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.phylog(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.phylog(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75)
plot.phylog(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.phylog(taxo2phylog(as.taxo(taxo.eg[[2]])), clabel.l = 1,
clabel.n = 0.75, f = 0.65)
## End(Not run)
> library(ade4)
> ### Name: newick2phylog
> ### Title: Create phylogeny
> ### Aliases: newick2phylog hclust2phylog taxo2phylog newick2phylog.addtools
> ### Keywords: manip
>
> ### ** Examples
>
>
> w <- "((((,,),,(,)),),(,));"
> w.phy <- newick2phylog(w)
> print(w.phy)
Phylogenetic tree with 9 leaves and 6 nodes
$class: phylog
$call: newick2phylog(x.tre = w)
$tre: ((((Ext1,Ext2,Ext3)I1,Ext...Ext7)I4,(Ext8,Ext9)I5)Root;
class length content
$leaves numeric 9 length of the first preceeding adjacent edge
$nodes numeric 6 length of the first preceeding adjacent edge
$parts list 6 subsets of descendant nodes
$paths list 15 path from root to node or leave
$droot numeric 15 distance to root
class dim content
$Wmat matrix 9-9 W matrix : root to the closest ancestor
$Wdist dist 36 Nodal distances
$Wvalues numeric 8 Eigen values of QWQ/sum(Q)
$Wscores data.frame 9-8 Eigen vectors of QWQ '1/n' normed
$Amat matrix 9-9 Topological proximity matrix A
$Avalues numeric 8 Eigen values of QAQ matrix
$Adim integer 1 number of positive eigen values of QAQ
$Ascores data.frame 9-8 Eigen vectors of QAQ '1/n' normed
$Aparam data.frame 6-3 Topological indices for nodes
$Bindica data.frame 9-8 class indicator from nodes
$Bscores data.frame 9-8 Topological orthonormal basis '1/n' normed
$Blabels character 6 Nodes labelling from orthonormal basis
> plot(w.phy)
> > > # 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
Phylogenetic tree with 500 leaves and 437 nodes
$class: phylog
$call: newick2phylog(x.tre = w, add.tools = FALSE)
$tre: (Ext1,((((((((((((((((Ext...35,Ext499)I436,Ext500)Root;
class length content
$leaves numeric 500 length of the first preceeding adjacent edge
$nodes numeric 437 length of the first preceeding adjacent edge
$parts list 437 subsets of descendant nodes
$paths list 937 path from root to node or leave
$droot numeric 937 distance to root
> radial.phylog(phy1, clabel.l = 0, circle = 2.2, clea = 0.5,
+ cnod = 0.5)
> data(newick.eg) > radial.phylog(newick2phylog(newick.eg[[8]], FALSE), cnode = 1, + clabel.l = 0.8) > > # hclust2phylog > data(USArrests) > hc <- hclust(dist(USArrests), "ave") > par(mfrow = c(1,2)) > plot(hc, hang = -1)
> phy <- hclust2phylog(hc) > plot.phylog(phy, clabel.l = 0.75, clabel.n = 0.6, f = 0.75)
>
> par(mfrow = c(1,1))
> row.names(USArrests)
[1] "Alabama" "Alaska" "Arizona" "Arkansas"
[5] "California" "Colorado" "Connecticut" "Delaware"
[9] "Florida" "Georgia" "Hawaii" "Idaho"
[13] "Illinois" "Indiana" "Iowa" "Kansas"
[17] "Kentucky" "Louisiana" "Maine" "Maryland"
[21] "Massachusetts" "Michigan" "Minnesota" "Mississippi"
[25] "Missouri" "Montana" "Nebraska" "Nevada"
[29] "New Hampshire" "New Jersey" "New Mexico" "New York"
[33] "North Carolina" "North Dakota" "Ohio" "Oklahoma"
[37] "Oregon" "Pennsylvania" "Rhode Island" "South Carolina"
[41] "South Dakota" "Tennessee" "Texas" "Utah"
[45] "Vermont" "Virginia" "Washington" "West Virginia"
[49] "Wisconsin" "Wyoming"
> names(phy$leaves) #WARNING not the same for two reasons
[1] "Florida" "North_Carolina" "California" "Maryland"
[5] "Arizona" "New_Mexico" "Delaware" "Alabama"
[9] "Louisiana" "Illinois" "New_York" "Michigan"
[13] "Nevada" "Alaska" "Mississippi" "South_Carolina"
[17] "Washington" "Oregon" "Wyoming" "Oklahoma"
[21] "Virginia" "Rhode_Island" "Massachusetts" "New_Jersey"
[25] "Missouri" "Arkansas" "Tennessee" "Georgia"
[29] "Colorado" "Texas" "Idaho" "Nebraska"
[33] "Kentucky" "Montana" "Ohio" "Utah"
[37] "Indiana" "Kansas" "Connecticut" "Pennsylvania"
[41] "Hawaii" "West_Virginia" "Maine" "South_Dakota"
[45] "North_Dakota" "Vermont" "Minnesota" "Wisconsin"
[49] "Iowa" "New_Hampshire"
> row.names(USArrests) <- gsub(" ","_",row.names(USArrests))
> row.names(USArrests)
[1] "Alabama" "Alaska" "Arizona" "Arkansas"
[5] "California" "Colorado" "Connecticut" "Delaware"
[9] "Florida" "Georgia" "Hawaii" "Idaho"
[13] "Illinois" "Indiana" "Iowa" "Kansas"
[17] "Kentucky" "Louisiana" "Maine" "Maryland"
[21] "Massachusetts" "Michigan" "Minnesota" "Mississippi"
[25] "Missouri" "Montana" "Nebraska" "Nevada"
[29] "New_Hampshire" "New_Jersey" "New_Mexico" "New_York"
[33] "North_Carolina" "North_Dakota" "Ohio" "Oklahoma"
[37] "Oregon" "Pennsylvania" "Rhode_Island" "South_Carolina"
[41] "South_Dakota" "Tennessee" "Texas" "Utah"
[45] "Vermont" "Virginia" "Washington" "West_Virginia"
[49] "Wisconsin" "Wyoming"
> names(phy$leaves) #WARNING not the same for one reason
[1] "Florida" "North_Carolina" "California" "Maryland"
[5] "Arizona" "New_Mexico" "Delaware" "Alabama"
[9] "Louisiana" "Illinois" "New_York" "Michigan"
[13] "Nevada" "Alaska" "Mississippi" "South_Carolina"
[17] "Washington" "Oregon" "Wyoming" "Oklahoma"
[21] "Virginia" "Rhode_Island" "Massachusetts" "New_Jersey"
[25] "Missouri" "Arkansas" "Tennessee" "Georgia"
[29] "Colorado" "Texas" "Idaho" "Nebraska"
[33] "Kentucky" "Montana" "Ohio" "Utah"
[37] "Indiana" "Kansas" "Connecticut" "Pennsylvania"
[41] "Hawaii" "West_Virginia" "Maine" "South_Dakota"
[45] "North_Dakota" "Vermont" "Minnesota" "Wisconsin"
[49] "Iowa" "New_Hampshire"
> USArrests <- USArrests[names(phy$leaves),]
> row.names(USArrests)
[1] "Florida" "North_Carolina" "California" "Maryland"
[5] "Arizona" "New_Mexico" "Delaware" "Alabama"
[9] "Louisiana" "Illinois" "New_York" "Michigan"
[13] "Nevada" "Alaska" "Mississippi" "South_Carolina"
[17] "Washington" "Oregon" "Wyoming" "Oklahoma"
[21] "Virginia" "Rhode_Island" "Massachusetts" "New_Jersey"
[25] "Missouri" "Arkansas" "Tennessee" "Georgia"
[29] "Colorado" "Texas" "Idaho" "Nebraska"
[33] "Kentucky" "Montana" "Ohio" "Utah"
[37] "Indiana" "Kansas" "Connecticut" "Pennsylvania"
[41] "Hawaii" "West_Virginia" "Maine" "South_Dakota"
[45] "North_Dakota" "Vermont" "Minnesota" "Wisconsin"
[49] "Iowa" "New_Hampshire"
> names(phy$leaves) #the same
[1] "Florida" "North_Carolina" "California" "Maryland"
[5] "Arizona" "New_Mexico" "Delaware" "Alabama"
[9] "Louisiana" "Illinois" "New_York" "Michigan"
[13] "Nevada" "Alaska" "Mississippi" "South_Carolina"
[17] "Washington" "Oregon" "Wyoming" "Oklahoma"
[21] "Virginia" "Rhode_Island" "Massachusetts" "New_Jersey"
[25] "Missouri" "Arkansas" "Tennessee" "Georgia"
[29] "Colorado" "Texas" "Idaho" "Nebraska"
[33] "Kentucky" "Montana" "Ohio" "Utah"
[37] "Indiana" "Kansas" "Connecticut" "Pennsylvania"
[41] "Hawaii" "West_Virginia" "Maine" "South_Dakota"
[45] "North_Dakota" "Vermont" "Minnesota" "Wisconsin"
[49] "Iowa" "New_Hampshire"
> 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.phylog(tax.phy, clabel.l = 1.25, clabel.n = 1.25, f = 0.75) > plot.phylog(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.phylog(taxo2phylog(as.taxo(taxo.eg[[2]])), clabel.l = 1, + clabel.n = 0.75, f = 0.65)
> > > >