Create phylogeny

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 (see the phylip software)

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

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

See also

phylog, plot.phylog, as.taxo

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)


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)
}