Nothing
Phylogenetic tree manipulation"
In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies
if (!requireNamespace("rmarkdown", quietly = TRUE) ||
!rmarkdown::pandoc_available()) {
warning(call. = FALSE, "Pandoc not found, the vignettes is not built")
knitr::knit_exit()
}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
require(RRphylo)
options(rmarkdown.html_vignette.check_title = FALSE)
tm<-function(backbone,data,source.tree=NULL,
tip.ages = NULL, node.ages = NULL,age.offset=NULL,title){
# require(ape)
# require(phytools)
# require(manipulate)
backbone->tree
data->dat
source.tree->tree2
max(diag(vcv(tree)))->H
H-diag(vcv(tree))->ages
if(!is.null(age.offset)&&age.offset<0){
ages+abs(age.offset)->ages
H+abs(age.offset)->Hset
}else H->Hset
# if(is.null(min.branch)) min(tree$edge.length)->min.branch
#### DATA CHECK ####
if(!all(colnames(dat)%in%c("bind","reference","poly"))) {
if(any(is.na(as.logical(dat[,3])))) stop("Check columns order: it should be 'bind', 'reference', 'poly'")
warning("Colnames not matching: columns assumed to be ordered as 'bind','reference','poly'",immediate. = TRUE)
colnames(dat)<-c("bind","reference","poly")
}
if(!is.logical(dat$poly)) as.logical(dat$poly)->dat$poly
### Check for wrong poly assignment ###
if(any(apply(dat,1,function(k) (!grepl("-",k[2]))&!grepl("Genus",k[2])&!grepl("Clade",k[2])&as.logical(k[3])))){
warning("Found poly=TRUE at binding two tips, automatically changed to FALSE",immediate.=TRUE)
lapply(1:nrow(dat),function(k){
if((!grepl("-",dat[k,2]))&!grepl("Genus",k[k,2])&!grepl("Clade",k[k,2])&dat[k,3]){
dat[k,3]<<-FALSE
message(paste(" Please check",dat[k,1],"&",dat[k,2],"in your dataset",sep=" "))
}
})
}
### Check for genera and clades as bind ###
if(any(grepl("Genus",dat$bind))){
if(is.null(tree2)) stop("Please provide the source.tree")
sapply(1:nrow(dat),function(k){
if(grepl("Genus",dat[k,]$bind)){
trimws(gsub("Genus ","",dat[k,]$bind))->genref
getGenus(tree2,genref)->getgenref
if(getgenref[2]==1) dat[k,]$bind<<-grep(genref,tree2$tip.label,value=TRUE) else
dat[k,]$bind<<-paste(tips(tree2,getgenref[,3])[c(1,length(tips(tree2,getgenref[,3])))],collapse="-")
}
})
}
if(any(grepl("Clade",dat$bind))){
sapply(1:nrow(dat),function(k){
if(grepl("Clade",dat[k,]$bind)){
if(!gsub("Clade ","",dat[k,]$bind)%in%tree2$node.label) stop("Required node.label not indicated on the source.tree")
tips(tree2,Ntip(tree2)+which(tree2$node.label==gsub("Clade ","",dat[k,]$bind)))->claref
dat[k,]$bind<<-paste(claref[c(1,length(claref))],collapse="-")
}
})
}
data.frame(dat,bind.type=sapply(strsplit(dat[,1],"-"),length))->dat
if(any(dat$bind.type==2)&is.null(tree2)) stop("Please provide the source.tree")
### Check for genera and clades as references ###
if(any(grepl("Genus",dat$reference))){
sapply(1:nrow(dat),function(k){
if(grepl("Genus",dat[k,]$reference)){
trimws(gsub("Genus ","",dat[k,]$reference))->genref
try(getGenus(tree,genref),silent = TRUE)->getgenref
if(class(getgenref)!="try-error"){
if(getgenref[2]==1) dat[k,]$reference<<-grep(genref,tree$tip.label,value=TRUE) else
dat[k,]$reference<<-paste(tips(tree,getgenref[,3])[c(1,length(tips(tree,getgenref[,3])))],collapse="-")
}else stop(paste("Genus",genref,"missing from the backbone tree"))
# {
# try(getGenus(tree2,genref),silent = TRUE)->getgenref2
# if(class(getgenref2)!="try-error"){
# if(getgenref2[2]==1) dat[k,]$reference<<-grep(genref,tree2$tip.label,value=TRUE) else
# dat[k,]$reference<<-paste(tips(tree2,getgenref2[,3])[c(1,length(tips(tree2,getgenref2[,3])))],collapse="-")
# }else stop(paste("Genus",genref,"missing from the backbone and the source tree"))
# # {
# # if(any(grepl(genref,dat$bind[-k]))) dat[k,]$reference<<-paste(grep(paste(genref,"_",sep=""),dat$bind[-k],value=TRUE),collapse="-") else
# # stop(paste("Genus",genref,"missing from the backbone, the source and the tips to be attached"))
# # }
# }
}
})
}
if(any(grepl("Clade",dat$reference))){
sapply(1:nrow(dat),function(k){
if(grepl("Clade",dat[k,]$reference)){
if(!gsub("Clade ","",dat[k,]$reference)%in%tree$node.label) stop("Required node.label not indicated on the tree")
tips(tree,Ntip(tree)+which(tree$node.label==gsub("Clade ","",dat[k,]$reference)))->claref
dat[k,]$reference<<-paste(claref[c(1,length(claref))],collapse="-")
}
})
}
bind.all<-unlist(sapply(1:nrow(dat),function(x) {
ifelse(dat[x,4]==2,des<-tips(tree2,getMRCA(tree2,strsplit(dat[x,1],"-")[[1]])),des<-dat[x,1])
des
}))
if(any(duplicated(bind.all))) stop(paste(paste(bind.all[duplicated(bind.all)],collapse = ", "),"names duplicated in supplied tips"))
if(all(dat$bind.type==1)&(!is.null(tree2))) tree2<-NULL
# if(any(dat$bind%in%tree2$tip.label)) drop.tip(tree2,dat[which(dat$bind%in%tree2$tip.label),1])->tree2
dat$bind.tips<-NA
if(all(dat$bind.type==1)) dat$bind.tips<-dat$bind else{
dat[which(dat$bind.type==2),]$bind.tips<-lapply(dat$bind[which(dat$bind.type==2)],function(x) tips(tree2,getMRCA(tree2,strsplit(x,"-")[[1]])))
if(any(is.na(dat$bind.tips))) dat[which(is.na(dat$bind.tips)),]$bind.tips<-dat[which(is.na(dat$bind.tips)),]$bind
}
### bind missing from tree2 ###
if(!all(unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)){
stop(paste(paste(unlist(dat[which(dat$bind.type==2),]$bind.tips)[which(
unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)],
collapse=", "),"not in source.tree"))
}
### reference missing ###
if(!all(unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))){
stop(paste(paste(unlist(strsplit(dat$reference,"-"))[which(!unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))],
collapse=","),"missing from the backbone, the source and the tips to be attached"))
}
### bind already on the backbone ###
if(any(dat$bind%in%tree$tip.label)){
warning(paste(paste(dat[which(dat$bind%in%tree$tip.label),1],collapse=", "),"removed from the backbone tree"),immediate. = TRUE)
drop.tip(tree,dat[which(dat$bind%in%tree$tip.label),1])->tree
}
### duplicated reference ###
table(dat$reference)->tab.ref
if(any(tab.ref>1)){
for(j in 1:length(which(tab.ref>1))){
dat[which(dat$reference==names(which(tab.ref>1)[j])),]->ref.mult
# if(any(isTRUE(ref.mult$poly))) ref.mult[-which(isTRUE(ref.mult$poly)),]->ref.mult
if(any(ref.mult$poly)) ref.mult[which(!ref.mult$poly),]->ref.mult
paste(strsplit(ref.mult$reference[1],"-")[[1]][1],strsplit(ref.mult$bind[1],"-")[[1]][1],sep="-")->ref.mult$reference[-1]
# ref.mult[-1,]$poly<-TRUE
ref.mult$poly[-1]<-TRUE
dat[match(ref.mult$bind,dat$bind),]<-ref.mult
}
}
if(!is.null(tree2)){
dat$MRCAbind<-NA
sapply(dat[which(dat$bind.type==2),]$bind.tips,function(x) getMRCA(tree2,x))->dat$MRCAbind[which(dat$bind.type==2)]
if(any(dat$bind.type==2)){
unlist(sapply(dat[which(dat$bind.type==2),]$MRCAbind,function(x) tree$tip.label[which(tree$tip.label%in%tips(tree2,x))]))->remt
if(length(remt)>0){
drop.tip(tree,remt)->tree
ages[-match(remt,names(ages))]->ages
warning(paste(paste(remt,collapse=", "),"already on the source tree: removed from the backbone tree"),immediate. = TRUE)
}
}
}
### ordering ###
strsplit(dat$reference,"-")->refs
dat$ref.tree1<-NA
dat$ref.tree2<-NA
lapply(refs,function(x){
if(length(x[which(!x%in%tree$tip.label)])<1) NA else x[which(!x%in%tree$tip.label)]
})->ref.tree
dat[which(is.na(ref.tree)),][order(dat[which(is.na(ref.tree)),]$bind.type),]$ref.tree1<-seq(1,length(which(is.na(ref.tree))))
if(any(which(!is.na(ref.tree)))){
dat[which(!is.na(ref.tree)),]->dat.new
dat.new[,6:7]<-do.call(rbind,ref.tree[-which(is.na(ref.tree))])
if(any(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips))){
while(nrow(dat.new)>0){
which(!(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips)))->outs
if(length(outs)<1) stop("Recursive species attachment: check rows ",paste(rownames(dat.new),collapse = ", ")," in data")
dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<-max(dat$ref.tree1,na.rm=TRUE)+1:length(outs)
dat.new[-outs,]->dat.new
}
}else{
which(!(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips)))->outs
dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<-
max(dat$ref.tree1,na.rm=TRUE)+1:length(which(!dat.new$ref.tree1%in%dat.new[,1]))
}
}
dat[order(dat$ref.tree1),]->dat
### binding ###
for(k in 1:nrow(dat)){
if(length(strsplit(dat$reference,"-")[[k]])>1)
getMRCA(tree,strsplit(dat$reference,"-")[[k]])->where.ref else
which(tree$tip.label==strsplit(dat$reference,"-")[[k]])->where.ref
if(where.ref!=(Ntip(tree)+1)) tree$edge.length[which(tree$edge[,2]==where.ref)]->br.len else{
if(is.null(tree$root.edge)) tree$root.edge<-mean(tree$edge.length)
tree$root.edge->br.len
}
if(dat$bind.type[k]==1){
if(dat$poly[k]) 0->pos.ref else br.len/2->pos.ref
bind.tip(tree,dat$bind[k],where.ref,position = pos.ref,edge.length =br.len/2)->tree
}else{
extract.clade(tree2,dat$MRCAbind[k])->cla
if(dat$poly[k]){
0->pos.ref
if(where.ref==(Ntip(tree)+1)&&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>H)
# rescale(cla,"depth",(H+max(diag(vcv(cla)))/10))->cla else
rescaleRR(cla,height=(H+max(diag(vcv(cla)))/10))->cla else
if(where.ref!=(Ntip(tree)+1)&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))
# rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla
rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla
cla$root.edge<-max(diag(vcv(cla)))/10
}else {
if(where.ref==(Ntip(tree)+1)) br.len/2->pos.ref else {
max(diag(vcv(cla)))+br.len/2->Hcla
if((H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])<H/1000){
# rescale(cla,"depth",br.len/4)->cla
rescaleRR(cla,height=br.len/4)->cla
pos.ref<-br.len-br.len/4
}else{
if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),1])){
# rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla
rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla
pos.ref<-br.len/2
}else if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))
(max(diag(vcv(cla)))+br.len/2)-(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])->pos.ref else br.len/2->pos.ref
}
}
cla$root.edge<-br.len/2
}
bind.tree(tree,cla,where=where.ref,position = pos.ref)->tree
}
}
### tips calibration ages ###
if(is.null(tip.ages)){
rep(0,length(tree$tip.label))->tip.ages
names(tip.ages)<-tree$tip.label
tip.ages[match(names(ages),names(tip.ages))]<-ages
}else{
if(!all(names(ages)%in%names(tip.ages))) c(ages[which(!names(ages)%in%names(tip.ages))],tip.ages)->tip.ages
if(!all(tree$tip.label%in%names(tip.ages))){
rep(0,length(which(!tree$tip.label%in%names(tip.ages))))->tip.add
names(tip.add)<-tree$tip.label[which(!tree$tip.label%in%names(tip.ages))]
c(tip.ages,tip.add)->tip.ages
}
}
### nodes calibration ages ###
if(!is.null(node.ages)){
sapply(names(node.ages),function(x){
getMRCA(tree,unlist(strsplit(x,"-")))
})->names(node.ages)
}else node.ages<-c()
### age original root ###
if(!getMRCA(tree,names(ages))%in%names(node.ages)){
node.ages<-c(node.ages,Hset)
names(node.ages)[length(node.ages)]<-getMRCA(tree,names(ages))
}
### time distances inside attached clades ###
if(any(dat$bind.type==2)){
unlist(lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x){
c(x,getDescendants(tree2,x)[which(getDescendants(tree2,x)>Ntip(tree2))])->des
dist.nodes(tree2)->dn
max(diag(vcv(tree2)))-dn[which(rownames(dn)==(Ntip(tree2)+1)),match(des,rownames(dn))]->dndes
names(dndes)<-des
dndes
}))->ages.fix
if(!is.null(age.offset)&&age.offset>0) ages.fix+age.offset->ages.fix
sapply(names(ages.fix),function(x) getMRCA(tree,tips(tree2,as.numeric(x))))->names(ages.fix)
if(any(!names(ages.fix)%in%names(node.ages)))
c(ages.fix[which(!names(ages.fix)%in%names(node.ages))],node.ages)->node.ages
}
if(max(diag(vcv(tree)))>H&&(!(Ntip(tree)+1)%in%names(node.ages)))
warning(paste("Root age not indicated: the tree root arbitrarily set at",round(max(diag(vcv(tree))),2)),immediate.=TRUE)
scaleTree(tree,node.ages=node.ages,tip.ages =tip.ages)->tree.final->tree.plot
if(any(dat$bind.type==2)) lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x)
c(getMRCA(tree.plot,tips(tree2,x)),getDescendants(tree.plot,getMRCA(tree.plot,tips(tree2,x)))))->cla.plot else cla.plot<-c()
c(which(tree.plot$tip.label%in%dat$bind[which(dat$bind.type==1)]),unlist(cla.plot))->all.plot
# colo<-rep(scales::hue_pal()(2)[2],nrow(tree.plot$edge))
# colo[which(tree.plot$edge[,2]%in%all.plot)]<-scales::hue_pal()(2)[1]
colo<-rep("gray60",nrow(tree.plot$edge))
colo[which(tree.plot$edge[,2]%in%all.plot)]<-"red"
names(colo)<-tree.plot$edge[,2]
par(mar=c(2,0,1,0))
plot(tree.plot,edge.color=colo,edge.width=1.5,tip.color=colo[which(tree.plot$edge[,2]<=Ntip(tree.plot))])
title(title)
axisPhylo()
return(tree.final)
}
Index
- tree.merger tool
a. tree.merger basics
b. Input tree and data
c. Attaching individual tips to the backbone tree
d. Attaching clades to the backbone tree
e. Guided examples
- scaleTree tool
- cutPhylo tool
- fix.poly tool
tree.merger tool {#tree.merger}
tree.merger basics{#basics}
The function tree.merger is meant to merge phylogenetic information derived from different phylogenies into a single supertree. Given a backbone (backbone) and a source (source.tree) trees, tree.merger drops clades from the latter to attach them on the former according to the information provided in the dataset object data. Individual tips to add can be indicated in data as well. Once the supertree is assembled, tips and nodes ages are calibrated based on user-specified values.
Input tree and data{#data}
The backbone phylogeny serves as the reference to locate where single tips or entire clades extracted from the source.tree have to be attached. The backbone is assumed to be correctly calibrated so that nodes and tips ages (including the age of the tree root) are left unchanged, unless the user specifies otherwise. The source.tree is the phylogeny where the clades to add are extracted from. For each clade attached to the backbone, the time distances between the most recent common ancestor of the clade and its descendant nodes are kept fixed, unless the ages for any of these nodes are indicated by the user. All the new tips added to the backbone, irrespective of whether they are attached as a clade or as individual tips, are placed at the maximum distance from the tree root, unless calibration ages are supplied by the user. The data object is a dataframe including information about "what" is attached, where and how. data must be made of three columns:
-
bind: the tips or clades to be attached;
-
reference: the tips or clades where bind will be attached;
-
poly: a logical indicating whether the bind and reference pair should form a polytomy.
If different column names are supplied, tree.merger assumes they are ordered as described and eventually fails if this requirement is not met. Similarly, with duplicated bind supplied the function stops and throws an error message. A clade, either to be bound or to be the reference, must be indicated by collating the names of the two phylogenetically furthest tips belonging to it, separated by the "-" symbol. Alternatively, if backbone$node.label/source.tree$node.label is not NULL, a bind/reference clade can be indicated as "Clade NAMEOFTHECLADE" when appropriate. Similarly, an entire genus on both the backbone and the source.tree can be indicated as "Genus NAMEOFTHEGENUS". Regardless the way it was attached, any 'bound' tip can be used as a reference for another tip (individually or as an element for clade identification, i.e. in the "species1-species2" form). The order with which clades and tips to attach are supplied does not matter.
Tips and nodes are calibrated within tree.merger by means of the function scaleTree. To this aim, named vectors of tips and nodes ages, meant as time distance from the youngest tips within the phylogeny, must be supplied. As for the data object, the nodes to be calibrated should be identified by collating the names of the two phylogenetically furthest tips it subtends to, separated by a "-".
Attaching individual tips to the backbone tree{#individual}
If only individual tips are attached the source.tree can be left unspecified. Tips set to be attached to the same reference with poly=FALSE are considered to represent a polytomy. Tips set as bind which are already on the backbone tree are removed from the latter and placed according to the reference. In the example below, tips "genusE_1a" and "genusE_1b" are set to be attached to the same reference "genusE_1", creating a polytomy. The species "genusC_4" and "genusC_5", are both set to be bound to the entire "Genus genusC" (including "genusC_1", "genusC_2", and "genusC_3"), but only the latter is explicitly indicated to create a polytomous clade ("poly=TRUE"). Once "genusC_5" is attached, the most recent common ancestor (MRCA) of the entire genusC changes with respect to the MRCA on the backbone, hence the reference for "genusC_6" is identified by selecting the two phylogenetically furthest tips within the 'new' genusC, that is "genusC_1-genusC_5". "genusB_3" belonging to the backbone is indicated to be moved, and "genusH_1" is added to the tree root thus changing the total height of the tree.
require(ape)
require(phytools)
set.seed(14)
rtree(10,tip.label=c("genusB_1","genusD_1","genusB_2","genusA_1","genusC_1",
"genusE_1","genusC_2","genusD_2","genusB_3","genusC_3"))->tree.back
tree.back$node.label[6]<-"DC"
par(mar=c(2,3.5,1,3.5))
plot(tree.back,edge.width=1.2)
nodelabels(text=tree.back$node.label[6],node=Ntip(tree.back)+6,col="forestgreen",frame="n",adj=0)
title("backbone tree")
axisPhylo()
data.frame(bind=c("genusE_1a","genusC_3a","genusB_1a","genusC_4","genusF_1",
"genusG_1","genusH_1","genusC_5","genusC_6","genusB_3","genusE_1b"),
reference=c("genusE_1","genusC_3","genusB_1","Genus genusC","Clade DC",
"genusF_1-genusB_2","genusE_1a-genusC_3","Genus genusC",
"genusC_5-genusC_1",
"genusB_2-genusB_1","genusE_1"),
poly=c(FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE))->dato
require(kableExtra)
knitr::kable(dato,align="c") %>%
kable_styling(full_width = FALSE, position = "float_left") %>%
add_header_above(c("dato" = 3))
tree.merger(backbone=tree.back,data=dato,plot=FALSE)
suppressWarnings(tm(backbone=tree.back,data=dato,title="merged tree"))
As no tip.ages are supplied to tree.merger, all the new tips are placed at the maximum distance from the tree root. Since no age for the root of the merged tree is indicated, the function places it arbitrarly and produces a warning to inform the user about its position with respect to the youngest tip on the phylogeny.
To calibrate the the ages of either tips or nodes within the merged tree, the arguments tip.ages and node.ages must be indicated.
c(1,2,1.7,1.5,0.8,1.5,0.3,1.2,0.2)->ages.tip
c("genusH_1","genusE_1a","genusE_1","genusE_1b","genusF_1","genusC_5","genusC_3a","genusG_1","genusB_1a")->names(ages.tip)
c(2.2,2.9,3.5)->ages.node
c("genusB_1-genusF_1","genusE_1a-genusE_1b","genusH_1-genusB_1")->names(ages.node)
ages.tip
ages.node
tree.merger(backbone=tree.back,data=dato,tip.ages=ages.tip,node.ages = ages.node,plot=FALSE)
suppressWarnings(tm(backbone=tree.back,data=dato,tip.ages=ages.tip,node.ages = ages.node,title="merged and calibrated tree"))
Attaching clades to the backbone tree{#clades}
When a clade is attached, the node subtending to it on source.tree is identified as the MRCA of the tip pair, the "Genus", or the "Clade" indicated in bind. In the example below, "Genus genusA" from the source is added as sister to "genusA_1" within the backbone. Then, "genusL_1" is bound to the newly created clade made of all the tips belonging to the "genusA", located by the two phylogenetically furthest tips within it.
set.seed(1)
rtree(10,tip.label=c("genusH_1","genusA_3","genusA_4","genusJ_1","genusI_1",
"genusG_1","genusA_2","genusK_1","genusF_1","genusF_2"))->tree.source
tree.source$node.labels[7]<-"HI"
par(mfrow=c(1,2),mar=c(2,0,1,0))
plot(tree.back,edge.width=1.8)
nodelabels(text=tree.back$node.label[6],node=Ntip(tree.back)+6,col="forestgreen",frame="n",adj=0)
title("backbone tree")
axisPhylo()
plot(tree.source,edge.width=1.8)
nodelabels(text=tree.source$node.label[7],node=Ntip(tree.source)+7,col="forestgreen",frame="n",adj=0)
title("source tree")
axisPhylo()
data.frame(bind=c("Genus genusA","genusG_1-genusF_2","Clade HI","genusL_1"),
reference=c("genusA_1","Clade DC","Genus genusB","genusA_1-genusA_4"),
poly=c(FALSE,FALSE,FALSE,FALSE))->dato.clade
knitr::kable(dato.clade,align="c") %>%
kable_styling(full_width = TRUE, position = "center") %>%
add_header_above(c("dato.clade" = 3))
tree.merger(backbone=tree.back,data=dato.clade,source.tree=tree.source,plot=FALSE)
tm(backbone=tree.back,data=dato.clade,source.tree=tree.source,title="merged tree")
Guided examples {#examples}
### load the RRphylo example dataset including Cetaceans tree
data("DataCetaceans")
DataCetaceans$treecet->treecet # phylogenetic tree
treecet$node.label[(131-Ntip(treecet))]<-"Crown Mysticeti" # assigning node labels
### Select two clades and some species to be removed
tips(treecet,131)->crown.Mysticetes
tips(treecet,193)->Delphininae
c("Aetiocetus_weltoni","Saghacetus_osiris",
"Zygorhiza_kochii","Ambulocetus_natans",
"Kentriodon_pernix","Kentriodon_schneideri","Kentriodon_obscurus",
"Eurhinodelphis_cristatus","Eurhinodelphis_bossi")->extinct
plot(treecet,show.tip.label = FALSE,no.margin=TRUE)
nodelabels(frame="n",col="blue",font=2,node=c(131,193),text=c("crown\nMysticetes","Delphininae"))
tiplabels(frame="circle",bg="red",cex=.3,text=rep("",length(c(crown.Mysticetes,Delphininae,extinct))),
tip=which(treecet$tip.label%in%c(crown.Mysticetes,Delphininae,extinct)))
### Create the backbone and source trees
drop.tip(treecet,c(crown.Mysticetes[-which(tips(treecet,131)%in%
c("Caperea_marginata","Eubalaena_australis"))],
Delphininae[-which(tips(treecet,193)=="Tursiops_aduncus")],extinct))->backtree
keep.tip(treecet,c(crown.Mysticetes,Delphininae,extinct))->sourcetree
### Create the data object
data.frame(bind=c("Clade Crown Mysticeti",
"Aetiocetus_weltoni",
"Saghacetus_osiris",
"Zygorhiza_kochii",
"Ambulocetus_natans",
"Genus Kentriodon",
"Sousa_chinensis-Delphinus_delphis",
"Kogia_sima",
"Eurhinodelphis_cristatus",
"Grampus_griseus",
"Eurhinodelphis_bossi"),
reference=c("Fucaia_buelli-Aetiocetus_weltoni",
"Aetiocetus_cotylalveus",
"Fucaia_buelli-Tursiops_truncatus",
"Saghacetus_osiris-Fucaia_buelli",
"Dalanistes_ahmedi-Fucaia_buelli",
"Phocoena_phocoena-Delphinus_delphis",
"Sotalia_fluviatilis",
"Kogia_breviceps",
"Eurhinodelphis_longirostris",
"Globicephala_melas-Pseudorca_crassidens",
"Eurhinodelphis_longirostris"),
poly=c(FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE,
FALSE))->dato
knitr::kable(dato,align="c") %>%
kable_styling(full_width = TRUE, position = "center") %>%
add_header_above(c("dato" = 3))
### Merge the backbone and the source trees according to dato without calibrating tip and node ages
tree.merger(backbone = backtree,data=dato,source.tree = sourcetree,plot=FALSE)
### Set tips and nodes calibration ages
c(Aetiocetus_weltoni=28.0,
Saghacetus_osiris=33.9,
Zygorhiza_kochii=34.0,
Ambulocetus_natans=40.4,
Kentriodon_pernix=15.9,
Kentriodon_schneideri=11.61,
Kentriodon_obscurus=13.65,
Eurhinodelphis_bossi=13.65,
Eurhinodelphis_cristatus=5.33)->tipages
c("Ambulocetus_natans-Fucaia_buelli"=52.6,
"Balaena_mysticetus-Caperea_marginata"=21.5)->nodeages
### Merge the backbone and the source trees and calibrate tips and nodes ages
tree.merger(backbone = backtree,data=dato,source.tree = sourcetree,
tip.ages=tipages,node.ages=nodeages,plot=FALSE)
scaleTree tool {#scaleTree}
The function scaleTree is a useful tool to deal with phylogenetic age calibration written around Gene Hunt's scalePhylo function (https://naturalhistory.si.edu/staff/gene-hunt). It rescales branches and leaves of the tree according to species and/or nodes calibration ages (meant as distance from the youngest tip within the tree).
If only species ages are supplied (argument tip.ages), the function changes leaves length, leaving node ages and internal branch lengths unaltered. When node ages are supplied (argument node.ages), the function shifts nodes position along their own branches while keeping other nodes and species positions unchanged.
library(ape)
library(phytools)
set.seed(14)
DataFelids$treefel->tree
tree$tip.label<-paste("t",seq(1:Ntip(tree)),sep="")
max(nodeHeights(tree))->H
sample(H-diag(vcv(tree)),8)->sp.ages
sp.ages+tree$edge.length[match(match(names(sp.ages),tree$tip.label),tree$edge[,2])]/2->sp.ages
sp.ages[c(3,7)]<-0
sp.ages
scaleTree(tree,tip.ages=sp.ages)->treeS1
edge.col<-rep("gray60",nrow(tree$edge))
edge.col[which(treeS1$edge[,2]%in%match(names(sp.ages),tree$tip.label))]<-"blue"
par(mfcol=c(2,2),mar=c(0.1,0.1,1,0.1))
plot(tree,edge.color = edge.col,edge.width=1.5,show.tip.label=F)
title("original",cex.main=1.2)
plot(treeS1,edge.color = edge.col,edge.width=1.5,show.tip.label=F)
title("species ages rescaled",cex.main=1.2)
set.seed(0)
sample(seq((Ntip(tree)+2),(Nnode(tree)+Ntip(tree))),8)->nods
H-dist.nodes(tree)[(Ntip(tree)+1),nods]->nod.ages
sapply(1:length(nods),function(x) {
H-dist.nodes(tree)[(Ntip(tree)+1),c(getMommy(tree,nods[x])[1],getDescendants(tree,nods[x])[1:2])]->par.ages
nod.ages[x]+((min(abs(nod.ages[x]-par.ages))-0.2)*sample(c(-1,1),1))
})->nod.ages
nod.ages
scaleTree(tree,node.ages=nod.ages)->treeS2
treeS2->treeS1
unlist(lapply(1:length(nods), function(x) c(nods[x],getDescendants(tree,nods[x])[1:2])))->brcol
edge.col<-rep("gray60",nrow(tree$edge))
edge.col[which(treeS1$edge[,2]%in%brcol)]<-"red"
#par(mfrow=c(2,1),mar=c(0.1,0.1,1,0.1))
plot(tree,edge.color = edge.col,edge.width=1.5,show.tip.label=F)
title("original",cex.main=1.2)
plot(treeS1,edge.color = edge.col,edge.width=1.5,show.tip.label=F)
title("node ages rescaled",cex.main=1.2)
It may happen that species and/or node ages to be calibrated are older than the age of their ancestors. In such cases, after moving the species (node) to its target age, the function reassembles the phylogeny above it by assigning the same branch length (set through the argument min.branch) to the all the branches along the species (node) path, so that the tree is well-conformed and ancestor-descendants relationships remain unchanged. In this way changes to the original tree topology only pertain to the path along the "calibrated" species.
H-dist.nodes(tree)[(Nnode(tree)+1),91]->sp.ages
names(sp.ages)<-tree$tip.label[1]
H-dist.nodes(tree)[(Nnode(tree)+1),164]->nod.ages
names(nod.ages)<-96
c(sp.ages,nod.ages)
# scaleTree(tree,tip.ages = sp.ages,node.ages = nod.ages,min.branch = 1)->treeS
scaleTree(tree,tip.ages = sp.ages,node.ages = nod.ages)->treeS
par(mfrow=c(1,2))
plot(tree,edge.color = "gray40",show.tip.label=F,no.margin = TRUE,edge.width=1.5)
plotinfo <- get("last_plot.phylo", envir = .PlotPhyloEnv)
points(plotinfo$xx[1],plotinfo$yy[1],pch=16,col="blue",cex=1.2)
points(plotinfo$xx[91],plotinfo$yy[1],pch=4,col="blue",cex=1.5,lwd=2)
text("target age",x= plotinfo$xx[91]-1,y=plotinfo$yy[1],adj=1,col="blue",cex=0.8)
points(plotinfo$xx[96],plotinfo$yy[96],pch=16,col="red",cex=1.2)
points(plotinfo$xx[164],plotinfo$yy[96],pch=4,col="red",cex=1.5,lwd=2)
text("target age",x= plotinfo$xx[164]-1,y=plotinfo$yy[96],adj=1,col="red",cex=0.8)
edge.col<-rep("gray40",nrow(tree$edge))
edge.col[which(treeS$edge[,2]%in%c(1,getMommy(tree,1)))]<-"blue"
edge.col[which(treeS$edge[,2]%in%c(94,95,96))]<-"red"
plot(treeS,edge.color = edge.col,show.tip.label=F,no.margin = TRUE,edge.width=1.5)
plotinfo <- get("last_plot.phylo", envir = .PlotPhyloEnv)
points(plotinfo$xx[1],plotinfo$yy[1],pch=16,col="blue",cex=1.2)
points(plotinfo$xx[96],plotinfo$yy[96],pch=16,col="red",cex=1.2)
Guided examples
# load the RRphylo example dataset including Felids tree
data("DataFelids")
DataFelids$treefel->tree
# get species and nodes ages
# (meant as distance from the youngest species, that is the Recent in this case)
max(nodeHeights(tree))->H
H-dist.nodes(tree)[(Ntip(tree)+1),(Ntip(tree)+1):(Ntip(tree)+Nnode(tree))]->age.nodes
H-diag(vcv(tree))->age.tips
# apply Pagel's lambda transformation to change node ages only
rescaleRR(tree,lambda=0.8)->tree1
# apply scaleTree to the transformed phylogeny, by setting
# the original ages at nodes as node.ages
scaleTree(tree1,node.ages=age.nodes)->treeS1
par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05))
plot(tree1,edge.color = "black",show.tip.label=F)
axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8)
title("lambda rescaled",cex.main=1.2)
plot(treeS1,edge.color = "black",show.tip.label=F)
axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8)
title("scaleTree rescaled",cex.main=1.2)
# change leaf length of 10 sampled species
tree->tree2
set.seed(14)
sample(tree2$tip.label,10)->sam.sp
age.tips[sam.sp]->age.sam
age.sam[which(age.sam>0.1)]<-age.sam[which(age.sam>0.1)]-1.5
age.sam[which(age.sam<0.1)]<-age.sam[which(age.sam<0.1)]+0.2
tree2$edge.length[match(match(sam.sp,tree$tip.label),tree$edge[,2])]<-age.sam
# apply scaleTree to the transformed phylogeny, by setting
# the original ages at sampled tips as tip.ages
scaleTree(tree2,tip.ages=age.tips[sam.sp])->treeS2
edge.col<-rep("black",nrow(tree$edge))
edge.col[which(treeS2$edge[,2]%in%match(sam.sp,tree$tip.label))]<-"red"
par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05))
plot(tree2,edge.color = edge.col,show.tip.label=F)
axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8)
title("leaves cut",cex.main=1.2)
plot(treeS2,edge.color = edge.col,show.tip.label=F)
axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8)
title("scaleTree rescaled",cex.main=1.2)
# apply Pagel's kappa transformation to change both species and node ages,
# including the age at the tree root
rescaleRR(tree,kappa=0.5)->tree3
# apply scaleTree to the transformed phylogeny, by setting
# the original ages at nodes as node.ages
scaleTree(tree1,tip.ages = age.tips,node.ages=age.nodes)->treeS3
par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05))
plot(tree3,edge.color = "black",show.tip.label=F)
axisPhylo(tck=-0.02,cex.axis=0.8)
title("kappa rescaled",cex.main=1.2)
plot(treeS3,edge.color = "black",show.tip.label=F)
axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8)
title("scaleTree rescaled",cex.main=1.2)
cutPhylo tool {#cutPhylo}
The function cutPhylo is meant to cut the phylogentic tree to remove all the tips and nodes younger than a reference (user-specified) age, which can also coincide with a specific node. When an entire clade is cut, the user can choose (by the argument keep.lineage) to keep its branch length as a tip of the new tree, or remove it completely.
DataFelids$treefel->tree
max(nodeHeights(tree))->H
par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05))
plot(tree,show.tip.label=F)
axis(side=1,at=seq(2,32,5),labels=rev(c(0,5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
abline(v=H-5,col="blue")
title("original",cex.main=1.2)
plot(tree,show.tip.label=F)
axis(side=1,at=seq(2,32,5),labels=rev(c(0,5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
title("original",cex.main=1.2)
points(plotinfo$xx[129],plotinfo$yy[129],pch=16,col="red",cex=1.2)
cutPhylo(tree,age=5,keep.lineage = TRUE)
cutPhylo(tree,age=5,keep.lineage = FALSE)
par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05))
age<-5
{
distNodes(tree,(Ntip(tree)+1))->dN
max(nodeHeights(tree))-age->cutT
dN[,2]->dd
dd[which(dd>=cutT)]->ddcut
names(ddcut)->cutter
### Tips only ###
tree->tt
if(all(cutter%in%tree$tip.label)){
tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]<-
tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]-(ddcut-cutT)
#}
}else{
### Tips and nodes ###
as.numeric(cutter[which(suppressWarnings(as.numeric(cutter))>Ntip(tree))])->cutn
i=1
while(i<=length(cutn)){
if(any(cutn%in%getDescendants(tree,cutn[i]))) cutn[-which(cutn%in%getDescendants(tree,cutn[i]))]->cutn
i=i+1
}
tree->tt
i=1
while(i<=length(cutn)){
getMRCA(tt,tips(tree,cutn[i]))->nn
drop.clade(tt,tips(tt,nn))->tt
tt$tip.label[which(tt$tip.label=="NA")]<-paste("l",i,sep="")
i=i+1
}
diag(vcv(tt))->times
if(any(times>cutT)){
times[which(times>cutT)]->times
tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]<-
tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]-(times-cutT)
}
}
tt->tt.age
plot(tt,show.tip.label=FALSE)
tiplabels(frame="n",col="blue",cex=.6,offset=0.5,
tip=which(!tt$tip.label%in%tree$tip.label),
text=tt$tip.label[which(!tt$tip.label%in%tree$tip.label)])
axis(side=1,at=seq(2,27,5),labels=rev(c(5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
title("cut at 5: keeping lineages",cex.main=1.2)
drop.tip(tt.age,which(!tt.age$tip.label%in%tree$tip.label))->tt.age
plot(tt.age,show.tip.label=FALSE)
axis(side=1,at=seq(2,27,5),labels=rev(c(5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
title("cut at 5: removing lineages",cex.main=1.2)
}
cutPhylo(tree,node=129,keep.lineage = TRUE)
cutPhylo(tree,node=129,keep.lineage = FALSE)
node<-129
{
distNodes(tree,(Ntip(tree)+1))->dN
dN[match(node,rownames(dN)),2]->cutT
dN[,2]->dd
dd[which(dd>=cutT)]->ddcut
names(ddcut)->cutter
### Tips only ###
tree->tt
if(all(cutter%in%tree$tip.label)){
tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]<-
tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]-(ddcut-cutT)
#}
}else{
### Tips and nodes ###
as.numeric(cutter[which(suppressWarnings(as.numeric(cutter))>Ntip(tree))])->cutn
i=1
while(i<=length(cutn)){
if(any(cutn%in%getDescendants(tree,cutn[i]))) cutn[-which(cutn%in%getDescendants(tree,cutn[i]))]->cutn
i=i+1
}
tree->tt
i=1
while(i<=length(cutn)){
getMRCA(tt,tips(tree,cutn[i]))->nn
drop.clade(tt,tips(tt,nn))->tt
tt$tip.label[which(tt$tip.label=="NA")]<-paste("l",i,sep="")
i=i+1
}
diag(vcv(tt))->times
if(any(times>cutT)){
times[which(times>cutT)]->times
tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]<-
tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]-(times-cutT)
}
}
tt->tt.node
par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05))
plot(tt,show.tip.label=FALSE)
tiplabels(frame="n",col="red",cex=.6,offset=0.5,
tip=which(!tt$tip.label%in%tree$tip.label),
text=tt$tip.label[which(!tt$tip.label%in%tree$tip.label)])
axis(side=1,at=seq(2,23.5,5),labels=rev(c(10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
title("cut at node: keeping lineages",cex.main=1.2)
drop.tip(tt.node,which(!tt.node$tip.label%in%tree$tip.label))->tt.node
plot(tt.node,show.tip.label=FALSE)
axis(side=1,at=seq(2,23.5,5),labels=rev(c(10,15,20,25,30)),tck=-0.02,cex.axis=0.8)
title("cut at node: removing lineages",cex.main=1.2)
}
fix.poly tool {#fix.poly}
The function fix.poly randomly resolves polytomies either at specified nodes or througout the tree (Castiglione et al. 2020). This latter feature works like ape's multi2di. However, contrary to the latter, polytomies are resolved to non-zero length branches, to provide credible partition of the evolutionary time among the nodes descending from the dichotomized node. This could be useful to gain realistic evolutionary rate estimates at applying RRphylo. Under the type = collapse specification the user is expected to indicate which node/s must be transformed into a multichotomus clade.
### load the RRphylo example dataset including Cetaceans tree
data("DataCetaceans")
DataCetaceans$treecet->treecet
### Resolve all the polytomies within Cetaceans phylogeny
fix.poly(treecet,type="resolve")->treecet.fixed
## Set branch colors
unlist(sapply(names(which(table(treecet$edge[,1])>2)),function(x)
c(x,getDescendants(treecet,as.numeric(x)))))->tocolo
unlist(sapply(names(which(table(treecet$edge[,1])>2)),function(x)
c(getMRCA(treecet.fixed,tips(treecet,x)),
getDescendants(treecet.fixed,as.numeric(getMRCA(treecet.fixed,tips(treecet,x)))))))->tocolo2
colo<-rep("gray60",nrow(treecet$edge))
names(colo)<-treecet$edge[,2]
colo2<-rep("gray60",nrow(treecet.fixed$edge))
names(colo2)<-treecet.fixed$edge[,2]
colo[match(tocolo,names(colo))]<-"red"
colo2[match(tocolo2,names(colo2))]<-"red"
par(mfrow=c(1,2))
plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3)
plot(treecet.fixed,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3)
### Resolve the polytomies pertaining the genus Kentriodon
fix.poly(treecet,type="resolve",node=221)->treecet.fixed2
## Set branch colors
c(221,getDescendants(treecet,as.numeric(221)))->tocolo
c(getMRCA(treecet.fixed2,tips(treecet,221)),
getDescendants(treecet.fixed2,as.numeric(getMRCA(treecet.fixed2,tips(treecet,221)))))->tocolo2
colo<-rep("gray60",nrow(treecet$edge))
names(colo)<-treecet$edge[,2]
colo2<-rep("gray60",nrow(treecet.fixed2$edge))
names(colo2)<-treecet.fixed2$edge[,2]
colo[match(tocolo,names(colo))]<-"red"
colo2[match(tocolo2,names(colo2))]<-"red"
par(mfrow=c(1,2))
plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3)
plot(treecet.fixed2,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3)
### Collapse Delphinidae into a polytomous clade
fix.poly(treecet,type="collapse",node=179)->treecet.collapsed
# Set branch colors
c(179,getDescendants(treecet,as.numeric(179)))->tocolo
c(getMRCA(treecet.collapsed,tips(treecet,179)),
getDescendants(treecet.collapsed,as.numeric(getMRCA(treecet.collapsed,tips(treecet,179)))))->tocolo2
colo<-rep("gray60",nrow(treecet$edge))
names(colo)<-treecet$edge[,2]
colo2<-rep("gray60",nrow(treecet.collapsed$edge))
names(colo2)<-treecet.collapsed$edge[,2]
colo[match(tocolo,names(colo))]<-"red"
colo2[match(tocolo2,names(colo2))]<-"red"
par(mfrow=c(1,2))
plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3)
plot(treecet.collapsed,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3)
References
Castiglione, S., Serio, C., Piccolo, M., Mondanaro, A., Melchionna, M., Di Febbraro, M., Sansalone, G., Wroe, S.,& Raia, P. (2020). The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals. Biological Journal of the Linnean Society, 132: 221-231.
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RRphylo documentation built on June 7, 2023, 5:49 p.m.
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if (!requireNamespace("rmarkdown", quietly = TRUE) || !rmarkdown::pandoc_available()) { warning(call. = FALSE, "Pandoc not found, the vignettes is not built") knitr::knit_exit() } knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) require(RRphylo) options(rmarkdown.html_vignette.check_title = FALSE) tm<-function(backbone,data,source.tree=NULL, tip.ages = NULL, node.ages = NULL,age.offset=NULL,title){ # require(ape) # require(phytools) # require(manipulate) backbone->tree data->dat source.tree->tree2 max(diag(vcv(tree)))->H H-diag(vcv(tree))->ages if(!is.null(age.offset)&&age.offset<0){ ages+abs(age.offset)->ages H+abs(age.offset)->Hset }else H->Hset # if(is.null(min.branch)) min(tree$edge.length)->min.branch #### DATA CHECK #### if(!all(colnames(dat)%in%c("bind","reference","poly"))) { if(any(is.na(as.logical(dat[,3])))) stop("Check columns order: it should be 'bind', 'reference', 'poly'") warning("Colnames not matching: columns assumed to be ordered as 'bind','reference','poly'",immediate. = TRUE) colnames(dat)<-c("bind","reference","poly") } if(!is.logical(dat$poly)) as.logical(dat$poly)->dat$poly ### Check for wrong poly assignment ### if(any(apply(dat,1,function(k) (!grepl("-",k[2]))&!grepl("Genus",k[2])&!grepl("Clade",k[2])&as.logical(k[3])))){ warning("Found poly=TRUE at binding two tips, automatically changed to FALSE",immediate.=TRUE) lapply(1:nrow(dat),function(k){ if((!grepl("-",dat[k,2]))&!grepl("Genus",k[k,2])&!grepl("Clade",k[k,2])&dat[k,3]){ dat[k,3]<<-FALSE message(paste(" Please check",dat[k,1],"&",dat[k,2],"in your dataset",sep=" ")) } }) } ### Check for genera and clades as bind ### if(any(grepl("Genus",dat$bind))){ if(is.null(tree2)) stop("Please provide the source.tree") sapply(1:nrow(dat),function(k){ if(grepl("Genus",dat[k,]$bind)){ trimws(gsub("Genus ","",dat[k,]$bind))->genref getGenus(tree2,genref)->getgenref if(getgenref[2]==1) dat[k,]$bind<<-grep(genref,tree2$tip.label,value=TRUE) else dat[k,]$bind<<-paste(tips(tree2,getgenref[,3])[c(1,length(tips(tree2,getgenref[,3])))],collapse="-") } }) } if(any(grepl("Clade",dat$bind))){ sapply(1:nrow(dat),function(k){ if(grepl("Clade",dat[k,]$bind)){ if(!gsub("Clade ","",dat[k,]$bind)%in%tree2$node.label) stop("Required node.label not indicated on the source.tree") tips(tree2,Ntip(tree2)+which(tree2$node.label==gsub("Clade ","",dat[k,]$bind)))->claref dat[k,]$bind<<-paste(claref[c(1,length(claref))],collapse="-") } }) } data.frame(dat,bind.type=sapply(strsplit(dat[,1],"-"),length))->dat if(any(dat$bind.type==2)&is.null(tree2)) stop("Please provide the source.tree") ### Check for genera and clades as references ### if(any(grepl("Genus",dat$reference))){ sapply(1:nrow(dat),function(k){ if(grepl("Genus",dat[k,]$reference)){ trimws(gsub("Genus ","",dat[k,]$reference))->genref try(getGenus(tree,genref),silent = TRUE)->getgenref if(class(getgenref)!="try-error"){ if(getgenref[2]==1) dat[k,]$reference<<-grep(genref,tree$tip.label,value=TRUE) else dat[k,]$reference<<-paste(tips(tree,getgenref[,3])[c(1,length(tips(tree,getgenref[,3])))],collapse="-") }else stop(paste("Genus",genref,"missing from the backbone tree")) # { # try(getGenus(tree2,genref),silent = TRUE)->getgenref2 # if(class(getgenref2)!="try-error"){ # if(getgenref2[2]==1) dat[k,]$reference<<-grep(genref,tree2$tip.label,value=TRUE) else # dat[k,]$reference<<-paste(tips(tree2,getgenref2[,3])[c(1,length(tips(tree2,getgenref2[,3])))],collapse="-") # }else stop(paste("Genus",genref,"missing from the backbone and the source tree")) # # { # # if(any(grepl(genref,dat$bind[-k]))) dat[k,]$reference<<-paste(grep(paste(genref,"_",sep=""),dat$bind[-k],value=TRUE),collapse="-") else # # stop(paste("Genus",genref,"missing from the backbone, the source and the tips to be attached")) # # } # } } }) } if(any(grepl("Clade",dat$reference))){ sapply(1:nrow(dat),function(k){ if(grepl("Clade",dat[k,]$reference)){ if(!gsub("Clade ","",dat[k,]$reference)%in%tree$node.label) stop("Required node.label not indicated on the tree") tips(tree,Ntip(tree)+which(tree$node.label==gsub("Clade ","",dat[k,]$reference)))->claref dat[k,]$reference<<-paste(claref[c(1,length(claref))],collapse="-") } }) } bind.all<-unlist(sapply(1:nrow(dat),function(x) { ifelse(dat[x,4]==2,des<-tips(tree2,getMRCA(tree2,strsplit(dat[x,1],"-")[[1]])),des<-dat[x,1]) des })) if(any(duplicated(bind.all))) stop(paste(paste(bind.all[duplicated(bind.all)],collapse = ", "),"names duplicated in supplied tips")) if(all(dat$bind.type==1)&(!is.null(tree2))) tree2<-NULL # if(any(dat$bind%in%tree2$tip.label)) drop.tip(tree2,dat[which(dat$bind%in%tree2$tip.label),1])->tree2 dat$bind.tips<-NA if(all(dat$bind.type==1)) dat$bind.tips<-dat$bind else{ dat[which(dat$bind.type==2),]$bind.tips<-lapply(dat$bind[which(dat$bind.type==2)],function(x) tips(tree2,getMRCA(tree2,strsplit(x,"-")[[1]]))) if(any(is.na(dat$bind.tips))) dat[which(is.na(dat$bind.tips)),]$bind.tips<-dat[which(is.na(dat$bind.tips)),]$bind } ### bind missing from tree2 ### if(!all(unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)){ stop(paste(paste(unlist(dat[which(dat$bind.type==2),]$bind.tips)[which( unlist(dat[which(dat$bind.type==2),]$bind.tips)%in%tree2$tip.label)], collapse=", "),"not in source.tree")) } ### reference missing ### if(!all(unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))){ stop(paste(paste(unlist(strsplit(dat$reference,"-"))[which(!unlist(strsplit(dat$reference,"-"))%in%c(tree$tip.label,unlist(dat$bind.tips),tree2$tip.label))], collapse=","),"missing from the backbone, the source and the tips to be attached")) } ### bind already on the backbone ### if(any(dat$bind%in%tree$tip.label)){ warning(paste(paste(dat[which(dat$bind%in%tree$tip.label),1],collapse=", "),"removed from the backbone tree"),immediate. = TRUE) drop.tip(tree,dat[which(dat$bind%in%tree$tip.label),1])->tree } ### duplicated reference ### table(dat$reference)->tab.ref if(any(tab.ref>1)){ for(j in 1:length(which(tab.ref>1))){ dat[which(dat$reference==names(which(tab.ref>1)[j])),]->ref.mult # if(any(isTRUE(ref.mult$poly))) ref.mult[-which(isTRUE(ref.mult$poly)),]->ref.mult if(any(ref.mult$poly)) ref.mult[which(!ref.mult$poly),]->ref.mult paste(strsplit(ref.mult$reference[1],"-")[[1]][1],strsplit(ref.mult$bind[1],"-")[[1]][1],sep="-")->ref.mult$reference[-1] # ref.mult[-1,]$poly<-TRUE ref.mult$poly[-1]<-TRUE dat[match(ref.mult$bind,dat$bind),]<-ref.mult } } if(!is.null(tree2)){ dat$MRCAbind<-NA sapply(dat[which(dat$bind.type==2),]$bind.tips,function(x) getMRCA(tree2,x))->dat$MRCAbind[which(dat$bind.type==2)] if(any(dat$bind.type==2)){ unlist(sapply(dat[which(dat$bind.type==2),]$MRCAbind,function(x) tree$tip.label[which(tree$tip.label%in%tips(tree2,x))]))->remt if(length(remt)>0){ drop.tip(tree,remt)->tree ages[-match(remt,names(ages))]->ages warning(paste(paste(remt,collapse=", "),"already on the source tree: removed from the backbone tree"),immediate. = TRUE) } } } ### ordering ### strsplit(dat$reference,"-")->refs dat$ref.tree1<-NA dat$ref.tree2<-NA lapply(refs,function(x){ if(length(x[which(!x%in%tree$tip.label)])<1) NA else x[which(!x%in%tree$tip.label)] })->ref.tree dat[which(is.na(ref.tree)),][order(dat[which(is.na(ref.tree)),]$bind.type),]$ref.tree1<-seq(1,length(which(is.na(ref.tree)))) if(any(which(!is.na(ref.tree)))){ dat[which(!is.na(ref.tree)),]->dat.new dat.new[,6:7]<-do.call(rbind,ref.tree[-which(is.na(ref.tree))]) if(any(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips))){ while(nrow(dat.new)>0){ which(!(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips)))->outs if(length(outs)<1) stop("Recursive species attachment: check rows ",paste(rownames(dat.new),collapse = ", ")," in data") dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<-max(dat$ref.tree1,na.rm=TRUE)+1:length(outs) dat.new[-outs,]->dat.new } }else{ which(!(dat.new[,6]%in%unlist(dat.new$bind.tips)|dat.new[,7]%in%unlist(dat.new$bind.tips)))->outs dat[match(dat.new[outs,1],dat[,1]),]$ref.tree1<- max(dat$ref.tree1,na.rm=TRUE)+1:length(which(!dat.new$ref.tree1%in%dat.new[,1])) } } dat[order(dat$ref.tree1),]->dat ### binding ### for(k in 1:nrow(dat)){ if(length(strsplit(dat$reference,"-")[[k]])>1) getMRCA(tree,strsplit(dat$reference,"-")[[k]])->where.ref else which(tree$tip.label==strsplit(dat$reference,"-")[[k]])->where.ref if(where.ref!=(Ntip(tree)+1)) tree$edge.length[which(tree$edge[,2]==where.ref)]->br.len else{ if(is.null(tree$root.edge)) tree$root.edge<-mean(tree$edge.length) tree$root.edge->br.len } if(dat$bind.type[k]==1){ if(dat$poly[k]) 0->pos.ref else br.len/2->pos.ref bind.tip(tree,dat$bind[k],where.ref,position = pos.ref,edge.length =br.len/2)->tree }else{ extract.clade(tree2,dat$MRCAbind[k])->cla if(dat$poly[k]){ 0->pos.ref if(where.ref==(Ntip(tree)+1)&&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>H) # rescale(cla,"depth",(H+max(diag(vcv(cla)))/10))->cla else rescaleRR(cla,height=(H+max(diag(vcv(cla)))/10))->cla else if(where.ref!=(Ntip(tree)+1)&(max(diag(vcv(cla)))+max(diag(vcv(cla)))/10)>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])) # rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]+max(diag(vcv(cla)))/10))->cla cla$root.edge<-max(diag(vcv(cla)))/10 }else { if(where.ref==(Ntip(tree)+1)) br.len/2->pos.ref else { max(diag(vcv(cla)))+br.len/2->Hcla if((H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])<H/1000){ # rescale(cla,"depth",br.len/4)->cla rescaleRR(cla,height=br.len/4)->cla pos.ref<-br.len-br.len/4 }else{ if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),1])){ # rescale(cla,"depth",(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla rescaleRR(cla,height=(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2]))->cla pos.ref<-br.len/2 }else if(Hcla>(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])) (max(diag(vcv(cla)))+br.len/2)-(H-nodeHeights(tree)[which(tree$edge[,2]==where.ref),2])->pos.ref else br.len/2->pos.ref } } cla$root.edge<-br.len/2 } bind.tree(tree,cla,where=where.ref,position = pos.ref)->tree } } ### tips calibration ages ### if(is.null(tip.ages)){ rep(0,length(tree$tip.label))->tip.ages names(tip.ages)<-tree$tip.label tip.ages[match(names(ages),names(tip.ages))]<-ages }else{ if(!all(names(ages)%in%names(tip.ages))) c(ages[which(!names(ages)%in%names(tip.ages))],tip.ages)->tip.ages if(!all(tree$tip.label%in%names(tip.ages))){ rep(0,length(which(!tree$tip.label%in%names(tip.ages))))->tip.add names(tip.add)<-tree$tip.label[which(!tree$tip.label%in%names(tip.ages))] c(tip.ages,tip.add)->tip.ages } } ### nodes calibration ages ### if(!is.null(node.ages)){ sapply(names(node.ages),function(x){ getMRCA(tree,unlist(strsplit(x,"-"))) })->names(node.ages) }else node.ages<-c() ### age original root ### if(!getMRCA(tree,names(ages))%in%names(node.ages)){ node.ages<-c(node.ages,Hset) names(node.ages)[length(node.ages)]<-getMRCA(tree,names(ages)) } ### time distances inside attached clades ### if(any(dat$bind.type==2)){ unlist(lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x){ c(x,getDescendants(tree2,x)[which(getDescendants(tree2,x)>Ntip(tree2))])->des dist.nodes(tree2)->dn max(diag(vcv(tree2)))-dn[which(rownames(dn)==(Ntip(tree2)+1)),match(des,rownames(dn))]->dndes names(dndes)<-des dndes }))->ages.fix if(!is.null(age.offset)&&age.offset>0) ages.fix+age.offset->ages.fix sapply(names(ages.fix),function(x) getMRCA(tree,tips(tree2,as.numeric(x))))->names(ages.fix) if(any(!names(ages.fix)%in%names(node.ages))) c(ages.fix[which(!names(ages.fix)%in%names(node.ages))],node.ages)->node.ages } if(max(diag(vcv(tree)))>H&&(!(Ntip(tree)+1)%in%names(node.ages))) warning(paste("Root age not indicated: the tree root arbitrarily set at",round(max(diag(vcv(tree))),2)),immediate.=TRUE) scaleTree(tree,node.ages=node.ages,tip.ages =tip.ages)->tree.final->tree.plot if(any(dat$bind.type==2)) lapply(dat$MRCAbind[which(dat$bind.type==2)],function(x) c(getMRCA(tree.plot,tips(tree2,x)),getDescendants(tree.plot,getMRCA(tree.plot,tips(tree2,x)))))->cla.plot else cla.plot<-c() c(which(tree.plot$tip.label%in%dat$bind[which(dat$bind.type==1)]),unlist(cla.plot))->all.plot # colo<-rep(scales::hue_pal()(2)[2],nrow(tree.plot$edge)) # colo[which(tree.plot$edge[,2]%in%all.plot)]<-scales::hue_pal()(2)[1] colo<-rep("gray60",nrow(tree.plot$edge)) colo[which(tree.plot$edge[,2]%in%all.plot)]<-"red" names(colo)<-tree.plot$edge[,2] par(mar=c(2,0,1,0)) plot(tree.plot,edge.color=colo,edge.width=1.5,tip.color=colo[which(tree.plot$edge[,2]<=Ntip(tree.plot))]) title(title) axisPhylo() return(tree.final) }
Index
- tree.merger tool a. tree.merger basics b. Input tree and data c. Attaching individual tips to the backbone tree d. Attaching clades to the backbone tree e. Guided examples
- scaleTree tool
- cutPhylo tool
- fix.poly tool
tree.merger tool {#tree.merger}
tree.merger basics{#basics}
The function tree.merger is meant to merge phylogenetic information derived from different phylogenies into a single supertree. Given a backbone (backbone) and a source (source.tree) trees, tree.merger drops clades from the latter to attach them on the former according to the information provided in the dataset object data. Individual tips to add can be indicated in data as well. Once the supertree is assembled, tips and nodes ages are calibrated based on user-specified values.
Input tree and data{#data}
The backbone phylogeny serves as the reference to locate where single tips or entire clades extracted from the source.tree have to be attached. The backbone is assumed to be correctly calibrated so that nodes and tips ages (including the age of the tree root) are left unchanged, unless the user specifies otherwise. The source.tree is the phylogeny where the clades to add are extracted from. For each clade attached to the backbone, the time distances between the most recent common ancestor of the clade and its descendant nodes are kept fixed, unless the ages for any of these nodes are indicated by the user. All the new tips added to the backbone, irrespective of whether they are attached as a clade or as individual tips, are placed at the maximum distance from the tree root, unless calibration ages are supplied by the user. The data object is a dataframe including information about "what" is attached, where and how. data must be made of three columns:
-
bind: the tips or clades to be attached;
-
reference: the tips or clades where bind will be attached;
-
poly: a logical indicating whether the bind and reference pair should form a polytomy.
If different column names are supplied, tree.merger assumes they are ordered as described and eventually fails if this requirement is not met. Similarly, with duplicated bind supplied the function stops and throws an error message. A clade, either to be bound or to be the reference, must be indicated by collating the names of the two phylogenetically furthest tips belonging to it, separated by the "-" symbol. Alternatively, if backbone$node.label/source.tree$node.label is not NULL, a bind/reference clade can be indicated as "Clade NAMEOFTHECLADE" when appropriate. Similarly, an entire genus on both the backbone and the source.tree can be indicated as "Genus NAMEOFTHEGENUS". Regardless the way it was attached, any 'bound' tip can be used as a reference for another tip (individually or as an element for clade identification, i.e. in the "species1-species2" form). The order with which clades and tips to attach are supplied does not matter.
Tips and nodes are calibrated within tree.merger by means of the function scaleTree. To this aim, named vectors of tips and nodes ages, meant as time distance from the youngest tips within the phylogeny, must be supplied. As for the data object, the nodes to be calibrated should be identified by collating the names of the two phylogenetically furthest tips it subtends to, separated by a "-".
Attaching individual tips to the backbone tree{#individual}
If only individual tips are attached the source.tree can be left unspecified. Tips set to be attached to the same reference with poly=FALSE are considered to represent a polytomy. Tips set as bind which are already on the backbone tree are removed from the latter and placed according to the reference. In the example below, tips "genusE_1a" and "genusE_1b" are set to be attached to the same reference "genusE_1", creating a polytomy. The species "genusC_4" and "genusC_5", are both set to be bound to the entire "Genus genusC" (including "genusC_1", "genusC_2", and "genusC_3"), but only the latter is explicitly indicated to create a polytomous clade ("poly=TRUE"). Once "genusC_5" is attached, the most recent common ancestor (MRCA) of the entire genusC changes with respect to the MRCA on the backbone, hence the reference for "genusC_6" is identified by selecting the two phylogenetically furthest tips within the 'new' genusC, that is "genusC_1-genusC_5". "genusB_3" belonging to the backbone is indicated to be moved, and "genusH_1" is added to the tree root thus changing the total height of the tree.
require(ape) require(phytools) set.seed(14) rtree(10,tip.label=c("genusB_1","genusD_1","genusB_2","genusA_1","genusC_1", "genusE_1","genusC_2","genusD_2","genusB_3","genusC_3"))->tree.back tree.back$node.label[6]<-"DC" par(mar=c(2,3.5,1,3.5)) plot(tree.back,edge.width=1.2) nodelabels(text=tree.back$node.label[6],node=Ntip(tree.back)+6,col="forestgreen",frame="n",adj=0) title("backbone tree") axisPhylo() data.frame(bind=c("genusE_1a","genusC_3a","genusB_1a","genusC_4","genusF_1", "genusG_1","genusH_1","genusC_5","genusC_6","genusB_3","genusE_1b"), reference=c("genusE_1","genusC_3","genusB_1","Genus genusC","Clade DC", "genusF_1-genusB_2","genusE_1a-genusC_3","Genus genusC", "genusC_5-genusC_1", "genusB_2-genusB_1","genusE_1"), poly=c(FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE))->dato require(kableExtra) knitr::kable(dato,align="c") %>% kable_styling(full_width = FALSE, position = "float_left") %>% add_header_above(c("dato" = 3))
tree.merger(backbone=tree.back,data=dato,plot=FALSE) suppressWarnings(tm(backbone=tree.back,data=dato,title="merged tree"))
As no tip.ages are supplied to tree.merger, all the new tips are placed at the maximum distance from the tree root. Since no age for the root of the merged tree is indicated, the function places it arbitrarly and produces a warning to inform the user about its position with respect to the youngest tip on the phylogeny.
To calibrate the the ages of either tips or nodes within the merged tree, the arguments tip.ages and node.ages must be indicated.
c(1,2,1.7,1.5,0.8,1.5,0.3,1.2,0.2)->ages.tip c("genusH_1","genusE_1a","genusE_1","genusE_1b","genusF_1","genusC_5","genusC_3a","genusG_1","genusB_1a")->names(ages.tip) c(2.2,2.9,3.5)->ages.node c("genusB_1-genusF_1","genusE_1a-genusE_1b","genusH_1-genusB_1")->names(ages.node) ages.tip ages.node
tree.merger(backbone=tree.back,data=dato,tip.ages=ages.tip,node.ages = ages.node,plot=FALSE) suppressWarnings(tm(backbone=tree.back,data=dato,tip.ages=ages.tip,node.ages = ages.node,title="merged and calibrated tree"))
Attaching clades to the backbone tree{#clades}
When a clade is attached, the node subtending to it on source.tree is identified as the MRCA of the tip pair, the "Genus", or the "Clade" indicated in bind. In the example below, "Genus genusA" from the source is added as sister to "genusA_1" within the backbone. Then, "genusL_1" is bound to the newly created clade made of all the tips belonging to the "genusA", located by the two phylogenetically furthest tips within it.
set.seed(1) rtree(10,tip.label=c("genusH_1","genusA_3","genusA_4","genusJ_1","genusI_1", "genusG_1","genusA_2","genusK_1","genusF_1","genusF_2"))->tree.source tree.source$node.labels[7]<-"HI" par(mfrow=c(1,2),mar=c(2,0,1,0)) plot(tree.back,edge.width=1.8) nodelabels(text=tree.back$node.label[6],node=Ntip(tree.back)+6,col="forestgreen",frame="n",adj=0) title("backbone tree") axisPhylo() plot(tree.source,edge.width=1.8) nodelabels(text=tree.source$node.label[7],node=Ntip(tree.source)+7,col="forestgreen",frame="n",adj=0) title("source tree") axisPhylo() data.frame(bind=c("Genus genusA","genusG_1-genusF_2","Clade HI","genusL_1"), reference=c("genusA_1","Clade DC","Genus genusB","genusA_1-genusA_4"), poly=c(FALSE,FALSE,FALSE,FALSE))->dato.clade knitr::kable(dato.clade,align="c") %>% kable_styling(full_width = TRUE, position = "center") %>% add_header_above(c("dato.clade" = 3))
tree.merger(backbone=tree.back,data=dato.clade,source.tree=tree.source,plot=FALSE) tm(backbone=tree.back,data=dato.clade,source.tree=tree.source,title="merged tree")
Guided examples {#examples}
### load the RRphylo example dataset including Cetaceans tree data("DataCetaceans") DataCetaceans$treecet->treecet # phylogenetic tree treecet$node.label[(131-Ntip(treecet))]<-"Crown Mysticeti" # assigning node labels ### Select two clades and some species to be removed tips(treecet,131)->crown.Mysticetes tips(treecet,193)->Delphininae c("Aetiocetus_weltoni","Saghacetus_osiris", "Zygorhiza_kochii","Ambulocetus_natans", "Kentriodon_pernix","Kentriodon_schneideri","Kentriodon_obscurus", "Eurhinodelphis_cristatus","Eurhinodelphis_bossi")->extinct plot(treecet,show.tip.label = FALSE,no.margin=TRUE) nodelabels(frame="n",col="blue",font=2,node=c(131,193),text=c("crown\nMysticetes","Delphininae")) tiplabels(frame="circle",bg="red",cex=.3,text=rep("",length(c(crown.Mysticetes,Delphininae,extinct))), tip=which(treecet$tip.label%in%c(crown.Mysticetes,Delphininae,extinct))) ### Create the backbone and source trees drop.tip(treecet,c(crown.Mysticetes[-which(tips(treecet,131)%in% c("Caperea_marginata","Eubalaena_australis"))], Delphininae[-which(tips(treecet,193)=="Tursiops_aduncus")],extinct))->backtree keep.tip(treecet,c(crown.Mysticetes,Delphininae,extinct))->sourcetree ### Create the data object data.frame(bind=c("Clade Crown Mysticeti", "Aetiocetus_weltoni", "Saghacetus_osiris", "Zygorhiza_kochii", "Ambulocetus_natans", "Genus Kentriodon", "Sousa_chinensis-Delphinus_delphis", "Kogia_sima", "Eurhinodelphis_cristatus", "Grampus_griseus", "Eurhinodelphis_bossi"), reference=c("Fucaia_buelli-Aetiocetus_weltoni", "Aetiocetus_cotylalveus", "Fucaia_buelli-Tursiops_truncatus", "Saghacetus_osiris-Fucaia_buelli", "Dalanistes_ahmedi-Fucaia_buelli", "Phocoena_phocoena-Delphinus_delphis", "Sotalia_fluviatilis", "Kogia_breviceps", "Eurhinodelphis_longirostris", "Globicephala_melas-Pseudorca_crassidens", "Eurhinodelphis_longirostris"), poly=c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE))->dato knitr::kable(dato,align="c") %>% kable_styling(full_width = TRUE, position = "center") %>% add_header_above(c("dato" = 3))
### Merge the backbone and the source trees according to dato without calibrating tip and node ages tree.merger(backbone = backtree,data=dato,source.tree = sourcetree,plot=FALSE) ### Set tips and nodes calibration ages c(Aetiocetus_weltoni=28.0, Saghacetus_osiris=33.9, Zygorhiza_kochii=34.0, Ambulocetus_natans=40.4, Kentriodon_pernix=15.9, Kentriodon_schneideri=11.61, Kentriodon_obscurus=13.65, Eurhinodelphis_bossi=13.65, Eurhinodelphis_cristatus=5.33)->tipages c("Ambulocetus_natans-Fucaia_buelli"=52.6, "Balaena_mysticetus-Caperea_marginata"=21.5)->nodeages ### Merge the backbone and the source trees and calibrate tips and nodes ages tree.merger(backbone = backtree,data=dato,source.tree = sourcetree, tip.ages=tipages,node.ages=nodeages,plot=FALSE)
scaleTree tool {#scaleTree}
The function scaleTree is a useful tool to deal with phylogenetic age calibration written around Gene Hunt's scalePhylo function (https://naturalhistory.si.edu/staff/gene-hunt). It rescales branches and leaves of the tree according to species and/or nodes calibration ages (meant as distance from the youngest tip within the tree).
If only species ages are supplied (argument tip.ages), the function changes leaves length, leaving node ages and internal branch lengths unaltered. When node ages are supplied (argument node.ages), the function shifts nodes position along their own branches while keeping other nodes and species positions unchanged.
library(ape) library(phytools) set.seed(14) DataFelids$treefel->tree tree$tip.label<-paste("t",seq(1:Ntip(tree)),sep="") max(nodeHeights(tree))->H sample(H-diag(vcv(tree)),8)->sp.ages sp.ages+tree$edge.length[match(match(names(sp.ages),tree$tip.label),tree$edge[,2])]/2->sp.ages sp.ages[c(3,7)]<-0 sp.ages scaleTree(tree,tip.ages=sp.ages)->treeS1 edge.col<-rep("gray60",nrow(tree$edge)) edge.col[which(treeS1$edge[,2]%in%match(names(sp.ages),tree$tip.label))]<-"blue" par(mfcol=c(2,2),mar=c(0.1,0.1,1,0.1)) plot(tree,edge.color = edge.col,edge.width=1.5,show.tip.label=F) title("original",cex.main=1.2) plot(treeS1,edge.color = edge.col,edge.width=1.5,show.tip.label=F) title("species ages rescaled",cex.main=1.2) set.seed(0) sample(seq((Ntip(tree)+2),(Nnode(tree)+Ntip(tree))),8)->nods H-dist.nodes(tree)[(Ntip(tree)+1),nods]->nod.ages sapply(1:length(nods),function(x) { H-dist.nodes(tree)[(Ntip(tree)+1),c(getMommy(tree,nods[x])[1],getDescendants(tree,nods[x])[1:2])]->par.ages nod.ages[x]+((min(abs(nod.ages[x]-par.ages))-0.2)*sample(c(-1,1),1)) })->nod.ages nod.ages scaleTree(tree,node.ages=nod.ages)->treeS2 treeS2->treeS1 unlist(lapply(1:length(nods), function(x) c(nods[x],getDescendants(tree,nods[x])[1:2])))->brcol edge.col<-rep("gray60",nrow(tree$edge)) edge.col[which(treeS1$edge[,2]%in%brcol)]<-"red" #par(mfrow=c(2,1),mar=c(0.1,0.1,1,0.1)) plot(tree,edge.color = edge.col,edge.width=1.5,show.tip.label=F) title("original",cex.main=1.2) plot(treeS1,edge.color = edge.col,edge.width=1.5,show.tip.label=F) title("node ages rescaled",cex.main=1.2)
It may happen that species and/or node ages to be calibrated are older than the age of their ancestors. In such cases, after moving the species (node) to its target age, the function reassembles the phylogeny above it by assigning the same branch length (set through the argument min.branch) to the all the branches along the species (node) path, so that the tree is well-conformed and ancestor-descendants relationships remain unchanged. In this way changes to the original tree topology only pertain to the path along the "calibrated" species.
H-dist.nodes(tree)[(Nnode(tree)+1),91]->sp.ages names(sp.ages)<-tree$tip.label[1] H-dist.nodes(tree)[(Nnode(tree)+1),164]->nod.ages names(nod.ages)<-96 c(sp.ages,nod.ages) # scaleTree(tree,tip.ages = sp.ages,node.ages = nod.ages,min.branch = 1)->treeS scaleTree(tree,tip.ages = sp.ages,node.ages = nod.ages)->treeS par(mfrow=c(1,2)) plot(tree,edge.color = "gray40",show.tip.label=F,no.margin = TRUE,edge.width=1.5) plotinfo <- get("last_plot.phylo", envir = .PlotPhyloEnv) points(plotinfo$xx[1],plotinfo$yy[1],pch=16,col="blue",cex=1.2) points(plotinfo$xx[91],plotinfo$yy[1],pch=4,col="blue",cex=1.5,lwd=2) text("target age",x= plotinfo$xx[91]-1,y=plotinfo$yy[1],adj=1,col="blue",cex=0.8) points(plotinfo$xx[96],plotinfo$yy[96],pch=16,col="red",cex=1.2) points(plotinfo$xx[164],plotinfo$yy[96],pch=4,col="red",cex=1.5,lwd=2) text("target age",x= plotinfo$xx[164]-1,y=plotinfo$yy[96],adj=1,col="red",cex=0.8) edge.col<-rep("gray40",nrow(tree$edge)) edge.col[which(treeS$edge[,2]%in%c(1,getMommy(tree,1)))]<-"blue" edge.col[which(treeS$edge[,2]%in%c(94,95,96))]<-"red" plot(treeS,edge.color = edge.col,show.tip.label=F,no.margin = TRUE,edge.width=1.5) plotinfo <- get("last_plot.phylo", envir = .PlotPhyloEnv) points(plotinfo$xx[1],plotinfo$yy[1],pch=16,col="blue",cex=1.2) points(plotinfo$xx[96],plotinfo$yy[96],pch=16,col="red",cex=1.2)
Guided examples
# load the RRphylo example dataset including Felids tree data("DataFelids") DataFelids$treefel->tree # get species and nodes ages # (meant as distance from the youngest species, that is the Recent in this case) max(nodeHeights(tree))->H H-dist.nodes(tree)[(Ntip(tree)+1),(Ntip(tree)+1):(Ntip(tree)+Nnode(tree))]->age.nodes H-diag(vcv(tree))->age.tips # apply Pagel's lambda transformation to change node ages only rescaleRR(tree,lambda=0.8)->tree1 # apply scaleTree to the transformed phylogeny, by setting # the original ages at nodes as node.ages scaleTree(tree1,node.ages=age.nodes)->treeS1 par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05)) plot(tree1,edge.color = "black",show.tip.label=F) axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8) title("lambda rescaled",cex.main=1.2) plot(treeS1,edge.color = "black",show.tip.label=F) axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8) title("scaleTree rescaled",cex.main=1.2) # change leaf length of 10 sampled species tree->tree2 set.seed(14) sample(tree2$tip.label,10)->sam.sp age.tips[sam.sp]->age.sam age.sam[which(age.sam>0.1)]<-age.sam[which(age.sam>0.1)]-1.5 age.sam[which(age.sam<0.1)]<-age.sam[which(age.sam<0.1)]+0.2 tree2$edge.length[match(match(sam.sp,tree$tip.label),tree$edge[,2])]<-age.sam # apply scaleTree to the transformed phylogeny, by setting # the original ages at sampled tips as tip.ages scaleTree(tree2,tip.ages=age.tips[sam.sp])->treeS2 edge.col<-rep("black",nrow(tree$edge)) edge.col[which(treeS2$edge[,2]%in%match(sam.sp,tree$tip.label))]<-"red" par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05)) plot(tree2,edge.color = edge.col,show.tip.label=F) axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8) title("leaves cut",cex.main=1.2) plot(treeS2,edge.color = edge.col,show.tip.label=F) axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8) title("scaleTree rescaled",cex.main=1.2) # apply Pagel's kappa transformation to change both species and node ages, # including the age at the tree root rescaleRR(tree,kappa=0.5)->tree3 # apply scaleTree to the transformed phylogeny, by setting # the original ages at nodes as node.ages scaleTree(tree1,tip.ages = age.tips,node.ages=age.nodes)->treeS3 par(mfrow=c(1,2),mar=c(1,0.1,1,0.1),mgp=c(3,0.1,0.05)) plot(tree3,edge.color = "black",show.tip.label=F) axisPhylo(tck=-0.02,cex.axis=0.8) title("kappa rescaled",cex.main=1.2) plot(treeS3,edge.color = "black",show.tip.label=F) axis(side=1,at=c(0,4,8,12,16,20,24,28,32),labels=rev(c(0,4,8,12,16,20,24,28,32)),tck=-0.02,cex.axis=0.8) title("scaleTree rescaled",cex.main=1.2)
cutPhylo tool {#cutPhylo}
The function cutPhylo is meant to cut the phylogentic tree to remove all the tips and nodes younger than a reference (user-specified) age, which can also coincide with a specific node. When an entire clade is cut, the user can choose (by the argument keep.lineage) to keep its branch length as a tip of the new tree, or remove it completely.
DataFelids$treefel->tree max(nodeHeights(tree))->H par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05)) plot(tree,show.tip.label=F) axis(side=1,at=seq(2,32,5),labels=rev(c(0,5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8) abline(v=H-5,col="blue") title("original",cex.main=1.2) plot(tree,show.tip.label=F) axis(side=1,at=seq(2,32,5),labels=rev(c(0,5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8) title("original",cex.main=1.2) points(plotinfo$xx[129],plotinfo$yy[129],pch=16,col="red",cex=1.2)
cutPhylo(tree,age=5,keep.lineage = TRUE) cutPhylo(tree,age=5,keep.lineage = FALSE)
par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05)) age<-5 { distNodes(tree,(Ntip(tree)+1))->dN max(nodeHeights(tree))-age->cutT dN[,2]->dd dd[which(dd>=cutT)]->ddcut names(ddcut)->cutter ### Tips only ### tree->tt if(all(cutter%in%tree$tip.label)){ tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]<- tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]-(ddcut-cutT) #} }else{ ### Tips and nodes ### as.numeric(cutter[which(suppressWarnings(as.numeric(cutter))>Ntip(tree))])->cutn i=1 while(i<=length(cutn)){ if(any(cutn%in%getDescendants(tree,cutn[i]))) cutn[-which(cutn%in%getDescendants(tree,cutn[i]))]->cutn i=i+1 } tree->tt i=1 while(i<=length(cutn)){ getMRCA(tt,tips(tree,cutn[i]))->nn drop.clade(tt,tips(tt,nn))->tt tt$tip.label[which(tt$tip.label=="NA")]<-paste("l",i,sep="") i=i+1 } diag(vcv(tt))->times if(any(times>cutT)){ times[which(times>cutT)]->times tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]<- tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]-(times-cutT) } } tt->tt.age plot(tt,show.tip.label=FALSE) tiplabels(frame="n",col="blue",cex=.6,offset=0.5, tip=which(!tt$tip.label%in%tree$tip.label), text=tt$tip.label[which(!tt$tip.label%in%tree$tip.label)]) axis(side=1,at=seq(2,27,5),labels=rev(c(5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8) title("cut at 5: keeping lineages",cex.main=1.2) drop.tip(tt.age,which(!tt.age$tip.label%in%tree$tip.label))->tt.age plot(tt.age,show.tip.label=FALSE) axis(side=1,at=seq(2,27,5),labels=rev(c(5,10,15,20,25,30)),tck=-0.02,cex.axis=0.8) title("cut at 5: removing lineages",cex.main=1.2) }
cutPhylo(tree,node=129,keep.lineage = TRUE) cutPhylo(tree,node=129,keep.lineage = FALSE)
node<-129 { distNodes(tree,(Ntip(tree)+1))->dN dN[match(node,rownames(dN)),2]->cutT dN[,2]->dd dd[which(dd>=cutT)]->ddcut names(ddcut)->cutter ### Tips only ### tree->tt if(all(cutter%in%tree$tip.label)){ tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]<- tt$edge.length[match(match(names(ddcut),tt$tip.label),tt$edge[,2])]-(ddcut-cutT) #} }else{ ### Tips and nodes ### as.numeric(cutter[which(suppressWarnings(as.numeric(cutter))>Ntip(tree))])->cutn i=1 while(i<=length(cutn)){ if(any(cutn%in%getDescendants(tree,cutn[i]))) cutn[-which(cutn%in%getDescendants(tree,cutn[i]))]->cutn i=i+1 } tree->tt i=1 while(i<=length(cutn)){ getMRCA(tt,tips(tree,cutn[i]))->nn drop.clade(tt,tips(tt,nn))->tt tt$tip.label[which(tt$tip.label=="NA")]<-paste("l",i,sep="") i=i+1 } diag(vcv(tt))->times if(any(times>cutT)){ times[which(times>cutT)]->times tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]<- tt$edge.length[match(match(names(times),tt$tip.label),tt$edge[,2])]-(times-cutT) } } tt->tt.node par(mfrow=c(1,2),mar=c(1,0.1,1.2,0.1),mgp=c(3,0.1,0.05)) plot(tt,show.tip.label=FALSE) tiplabels(frame="n",col="red",cex=.6,offset=0.5, tip=which(!tt$tip.label%in%tree$tip.label), text=tt$tip.label[which(!tt$tip.label%in%tree$tip.label)]) axis(side=1,at=seq(2,23.5,5),labels=rev(c(10,15,20,25,30)),tck=-0.02,cex.axis=0.8) title("cut at node: keeping lineages",cex.main=1.2) drop.tip(tt.node,which(!tt.node$tip.label%in%tree$tip.label))->tt.node plot(tt.node,show.tip.label=FALSE) axis(side=1,at=seq(2,23.5,5),labels=rev(c(10,15,20,25,30)),tck=-0.02,cex.axis=0.8) title("cut at node: removing lineages",cex.main=1.2) }
fix.poly tool {#fix.poly}
The function fix.poly randomly resolves polytomies either at specified nodes or througout the tree (Castiglione et al. 2020). This latter feature works like ape's multi2di. However, contrary to the latter, polytomies are resolved to non-zero length branches, to provide credible partition of the evolutionary time among the nodes descending from the dichotomized node. This could be useful to gain realistic evolutionary rate estimates at applying RRphylo. Under the type = collapse specification the user is expected to indicate which node/s must be transformed into a multichotomus clade.
### load the RRphylo example dataset including Cetaceans tree data("DataCetaceans") DataCetaceans$treecet->treecet ### Resolve all the polytomies within Cetaceans phylogeny fix.poly(treecet,type="resolve")->treecet.fixed ## Set branch colors unlist(sapply(names(which(table(treecet$edge[,1])>2)),function(x) c(x,getDescendants(treecet,as.numeric(x)))))->tocolo unlist(sapply(names(which(table(treecet$edge[,1])>2)),function(x) c(getMRCA(treecet.fixed,tips(treecet,x)), getDescendants(treecet.fixed,as.numeric(getMRCA(treecet.fixed,tips(treecet,x)))))))->tocolo2 colo<-rep("gray60",nrow(treecet$edge)) names(colo)<-treecet$edge[,2] colo2<-rep("gray60",nrow(treecet.fixed$edge)) names(colo2)<-treecet.fixed$edge[,2] colo[match(tocolo,names(colo))]<-"red" colo2[match(tocolo2,names(colo2))]<-"red" par(mfrow=c(1,2)) plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3) plot(treecet.fixed,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3) ### Resolve the polytomies pertaining the genus Kentriodon fix.poly(treecet,type="resolve",node=221)->treecet.fixed2 ## Set branch colors c(221,getDescendants(treecet,as.numeric(221)))->tocolo c(getMRCA(treecet.fixed2,tips(treecet,221)), getDescendants(treecet.fixed2,as.numeric(getMRCA(treecet.fixed2,tips(treecet,221)))))->tocolo2 colo<-rep("gray60",nrow(treecet$edge)) names(colo)<-treecet$edge[,2] colo2<-rep("gray60",nrow(treecet.fixed2$edge)) names(colo2)<-treecet.fixed2$edge[,2] colo[match(tocolo,names(colo))]<-"red" colo2[match(tocolo2,names(colo2))]<-"red" par(mfrow=c(1,2)) plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3) plot(treecet.fixed2,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3) ### Collapse Delphinidae into a polytomous clade fix.poly(treecet,type="collapse",node=179)->treecet.collapsed # Set branch colors c(179,getDescendants(treecet,as.numeric(179)))->tocolo c(getMRCA(treecet.collapsed,tips(treecet,179)), getDescendants(treecet.collapsed,as.numeric(getMRCA(treecet.collapsed,tips(treecet,179)))))->tocolo2 colo<-rep("gray60",nrow(treecet$edge)) names(colo)<-treecet$edge[,2] colo2<-rep("gray60",nrow(treecet.collapsed$edge)) names(colo2)<-treecet.collapsed$edge[,2] colo[match(tocolo,names(colo))]<-"red" colo2[match(tocolo2,names(colo2))]<-"red" par(mfrow=c(1,2)) plot(treecet,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo,edge.width=1.3) plot(treecet.collapsed,no.margin=TRUE,show.tip.label=FALSE,edge.color = colo2,edge.width=1.3)
References
Castiglione, S., Serio, C., Piccolo, M., Mondanaro, A., Melchionna, M., Di Febbraro, M., Sansalone, G., Wroe, S.,& Raia, P. (2020). The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals. Biological Journal of the Linnean Society, 132: 221-231.
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