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R/internalDendroFunctions.R
In clusterExperiment: Compare Clusterings for Single-Cell Sequencing
Defines functions
.force.ultrametric
.testPrint
.testPhyloObject
.addTreesToTips
.mergePhylo
.makeIntegerMatrix
.makeFakeBinary
.safePhyloSubset
.pruneToNodes
.convertToPhyClasses
.setNodeLabels
.getClusterIds
.matchToDendroData
.hasOutBranch
.makeSampleNames
.makeSampleNames<-function(x){paste("Sample",as.character(x))}
.clusterDendroColumns<-c("Position","ClusterIdDendro","ClusterIdMerge","NodeId")
.clusterSampleColumns<-c("Position","NodeId","SampleIndex")
.positionLevels<-c("cluster hierarchy node","cluster hierarchy tip","tip hierarchy","assigned tip","outbranch hierarchy node","unassigned tip","outbranch root")
.hasOutBranch<-function(object){
"outbranch root" %in% phylobase::tdata(object@dendro_samples)$Position
}
#' @description internal functions used by the package to manipulate dendrograms
#' @param inputValue a vector of values to match to dendro data
#' @param dendro a phylo4d object
#' @param matchColumn a character value giving the name of a column in the \code{tdata} of the dendro to match to. If "NodeIndex", means that will match to the row number (i.e. inputValue is a integer giving the row index); in this case it is the same as doing tdata(dendro)[inputValue,returnColumn]
#' @param returnColumn a character value giving the name of a column to return -- i.e. after matching to the matchColumn, return the corresponding values in the returnColumn. If returnColumn="NodeIndex", then just the index of the match is returned.
#' @noRd
.matchToDendroData<-function(inputValue,dendro,matchColumn="NodeId",returnColumn){
#Note that matchColumn="NodeIndex" means inputs give rows of the df. returnColumn="NodeIndex" means to return the index that matches (i.e. nodeIndex too)
df<-phylobase::tdata(dendro,type="all")
if(!is.character(returnColumn) || !is.character(matchColumn)) stop("coding error -- returnColumn and matchColumn must be character valued")
if(!returnColumn=="NodeIndex" && !returnColumn %in% names(df)) stop("coding error -- invalid value of returnColumn ")
if(!matchColumn=="NodeIndex" && !matchColumn %in% names(df)) stop("coding error -- invalid value of matchColumn")
if(!matchColumn=="NodeIndex") m<-match(inputValue, df[,matchColumn]) else m<-inputValue
if(any(is.na(m))) stop("coding error -- invalid value in inputValue (not in dendro)")
if(returnColumn=="NodeIndex") return(m)
else return(df[m,returnColumn])
}
.getClusterIds<-function(tipIndex,clusterDendro,returnValue=c("ClusterIdDendro","ClusterIdMerge")){
returnValue<-match.arg(returnValue)
tipNames <- .matchToDendroData(tipIndex,clusterDendro,matchColumn="NodeIndex",returnColumn=returnValue)
tipNames<-gsub("ClusterId","",as.character(tipNames))
return(tipNames)
}
#' @description phylo4d objects for cluster and sample dendrograms with pretty (and matched!) node and tip labels.
#' @param object a ClusterExperiment object
#' @param labelType. If 'id' returns the NodeId value for all the internal nodes that match the cluster dendrogram (cluster and sample dendrograms) and the cluster id for the tips (cluster dendrogram) or sample index for the tips (sample dendrogram). If "name", then the cluster ids and sample indices are converted into the cluster names (in the clusterMat) and the sample names (in colnames)
#' @param useMergeClusters if TRUE and there is an active merge, will remove the dendrogram cluster ids, and instead use merge cluster ids (which means will nave no label for dendrogram cluster merged)
#' @return Returns list of the two dendrograms with nodes that have been updated with names 'dendro_clusters' and 'dendro_samples'. Note they do not match requirement of the clusterExperiment object because have labels for nodes they "shouldn't".
#' @details Different from convertToPhyClasses, which is trying to get the needed info into the phylo or phylo4 class that doesn't have tdata. Calls that function internally
#' @noRd
.setNodeLabels<-function(object,labelType=c("name","id"),useMergeClusters=FALSE,overrideExistingNode=FALSE,singletonCluster=c("sample","cluster"),...){
labelType<-match.arg(labelType)
singletonCluster<-match.arg(singletonCluster)
if(!inherits(object,"ClusterExperiment")) stop("coding error -- function should be used for ClusterExperiment objects")
if(is.na(object@merge_index)|| all(is.na(phylobase::tdata(object@dendro_clusters)$ClusterIdMerge))) useMergeClusters<-FALSE
if(is.null(object@dendro_clusters)) return(NULL)
#internal option returns same as the .convertPhyClasses with both =TRUE
internalCluster<-.convertToPhyClasses(object@dendro_clusters, returnClass=c("phylo4d"), convertNodes=TRUE, convertTips=TRUE)
internalSamples<-.convertToPhyClasses(object@dendro_samples, returnClass=c("phylo4d"), convertNodes=TRUE, convertTips=TRUE)
if(useMergeClusters){
#erase all the dendro cluster Ids, which are only on the tips
whConvert<-which(!is.na(phylobase::tdata(internalCluster,type="tip")$ClusterIdDendro))
phylobase::tipLabels(internalCluster)[whConvert]<-NA
#now add merge cluster ids.
whConvert<-which(!is.na(phylobase::tdata(internalCluster,type="all")$ClusterIdMerge))
phylobase::labels(internalCluster)[whConvert] <- phylobase::tdata(internalCluster,type="all")$ClusterIdMerge[whConvert]
}
if(!overrideExistingNode){
#located here so merge labels won't be displayed if user changed that node name manually.
existingNodeLabels<-phylobase::nodeLabels(object@dendro_clusters)
whKeep<-which(!is.na(existingNodeLabels) & existingNodeLabels!=phylobase::tdata(internalCluster,type="internal")$NodeId)
phylobase::nodeLabels(internalCluster)[whKeep]<-existingNodeLabels[whKeep]
}
if(labelType=="name"){
###Convert to the name versions
if(useMergeClusters){
legMat<-clusterLegend(object)[[object@merge_index]]
labs<-phylobase::labels(internalCluster)[whConvert]
labs<-as.character(as.numeric(gsub("ClusterId","",labs)))
m<-match(labs,legMat[,"clusterIds"])
phylobase::labels(internalCluster)[whConvert]<-legMat[m,"name"]
}
else{
legMat<-clusterLegend(object)[[object@dendro_index]]
labs<-phylobase::tipLabels(internalCluster)
labs<-as.character(as.numeric(gsub("ClusterId","",labs)))
m<-match(labs,legMat[,"clusterIds"])
phylobase::tipLabels(internalCluster)<-legMat[m,"name"]
}
nms<-if(!is.null(colnames(object))) colnames(object) else .makeSampleNames(seq_len(ncol(object)))
phylobase::tipLabels(internalSamples) <- nms[as.numeric(phylobase::tipLabels(internalSamples))]
}
#Make sample node names match
type<-switch(singletonCluster,"sample"="internal","cluster"="all")
vals<-phylobase::tdata(internalSamples,type=type)$NodeId
wh<-which(!is.na(vals))
mToSample <- .matchToDendroData(inputValue=vals[wh], dendro=internalCluster, matchColumn="NodeId", returnColumn="NodeIndex")
phylobase::labels(internalSamples,type=type)[wh]<- phylobase::labels(internalCluster)[mToSample]
return(list(dendro_clusters=internalCluster,dendro_samples=internalSamples))
}
#' @param convertNodes logical. If true, the returned dendrogram will have the node labels change to be NodeId
#' @param convertTips logical. If true, the returned dendrogram will have the tip labels changed. If 'ClusterIdDendro' is in tdata (i.e. its a cluster dendrogram) then they are converted to Dendro cluster id (if no NAs) or if there are NAs, then merge cluster id (if dendros are NA in tips). If 'SampleIndex' is column name in tdata (i.e. is a samples dendrogram), then returns tip labels that are the SampleIndex value
#' @importFrom stats as.hclust
#' @importFrom ape as.phylo.hclust
#' @details phylo is class in ape package (S3). phylo4 and phylo4d are classes from phylobase package -- S4 version of phylo.
#' @noRd
.convertToPhyClasses<-function(x,returnClass=c("phylo4","phylo","phylo4d"),convertNodes=FALSE,convertTips=FALSE){
returnClass<-match.arg(returnClass)
if(inherits(x,"phylo4d") ){
if(returnClass %in% c("phylo","phylo4","phylo4d")){
#------
#Before convert,
#make internal node and cluster ids
#the node and tip labels (i.e. erase existing)
#------
if(convertNodes)
phylobase::nodeLabels(x)<-as.character(
phylobase::tdata(x,type="internal")$NodeId)
if(convertTips){
if("ClusterIdDendro" %in%
names(phylobase::tdata(x,type="all"))){
phylobase::tipLabels(x)<-as.character(
phylobase::tdata(x,type="tip")$ClusterIdDendro)
if(any(is.na(phylobase::tipLabels(x)))){
#this should mean its the cluster dendrogram limited to the merge ids.
phylobase::tipLabels(x)<-as.character(phylobase::tdata(x,type="tip")$ClusterIdMerge)
}
if(any(is.na(phylobase::tipLabels(x)))) stop("coding error -- even after accounting for merge id, still have NA values")
}
else if("SampleIndex" %in% names(phylobase::tdata(x,type="all")))
phylobase::tipLabels(x)<-as.character(phylobase::tdata(x,type="tip")$SampleIndex)
else stop("coding error -- tree should have either 'ClusterIdDendro' or 'SampleIndex' as names in tdata(x)")
}
}
if(returnClass %in% c("phylo4","phylo4d")) return(x)
}
if(!inherits(x,"phylo4d") & returnClass=="phylo4d") stop("coding error -- can't convert other classes to phylo4d at this time and still retain all correct information")
if(inherits(x,"dendrogram")){
x<-try(stats::as.hclust(x),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from dendrogram to hclust object. Reported error:",x)
}
if(inherits(x,"hclust")){
x<-try(ape::as.phylo.hclust(x),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from hclust to phylo object. Reported error:",x)
}
if(inherits(x,"phylo")){
if(returnClass=="phylo") return(x)
else{
## FIXME: getting warning here in test of plotCoClustering
## Commented out test for now, need to go back to it.
x<-try(as(x,"phylo4"),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from phylo to phylo4 object. Reported error:",x)
return(x)
}
}
if(inherits(x,"phylo4")){
if(returnClass=="phylo4") return(x)
else{
#phylobase warnings that trees with unknown edge order may be unsafe. This is probably because of this problem they ran into: http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2009-January/000353.html
#but the problem has probably been fixed by now in ape!
x<-try(suppressWarnings(as(x,"phylo")),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from phylo4 to phylo object. Reported error:",x)
#checkValidPhylo(x) returns NULL whether true or not.
return(x)
}
}
else{ stop("input x is not of hclust, dendrogram, phylo or phylo4 class")}
}
.pruneToNodes<-function(phylo4,nodesPruned){
##nodesPruned should be *the node numerical index* of those nodes that need "pruning" -- i.e. drop their children; other nodes kept the same.
tipsPruned<-unlist(phylobase::descendants(phylo4,node=nodesPruned,type="tip"),use.names=FALSE)
tipsKept<-phylobase::getNode(phylo4,type="tip")
tipsKept<-tipsKept[!tipsKept %in% tipsPruned]
nodesKeep<-c(nodesPruned,tipsKept)
allNodes<-phylobase::getNode(phylo4,type="all")
if(!all(nodesKeep %in% allNodes))
stop("nodes specified are not valid")
nodesKeep<-unique(unlist(phylobase::ancestors(phylo4,nodesKeep,"ALL"),use.names=FALSE)) #ALL means include self
names(nodesKeep)<-names(allNodes)[nodesKeep]
whEdgesKeep<-which(phylobase::edges(phylo4)[,2] %in% nodesKeep)
newEdge<-phylobase::edges(phylo4)[whEdgesKeep,]
#need to get rid of singleton nodes -- i.e. nodes with only 1 descendant
#this won't happen I think in my merge tree example, so make it error...
singletonNode<-if(length(which(table(newEdge[-which(newEdge[,1]==0),1])==1))>0) stop("coding error -- removing these nodes creates internal nodes that are singletons. Should be only choice of nodes that 'prunes' back the tree, not actually subsetting.")
#----------
#have to renumber everything so consecutive... technically documentation doesn't say that, but actually do (error otherwise)
#----------
#get the current numbers of tips, internal nodes, and root
#this is so know how to match the names, etc. back to them
newTips<-newEdge[which(!newEdge[,2] %in% newEdge[,1]),2]
newNodes<-nodesKeep
root<-newEdge[newEdge[,1] ==0,2]
whRoot<-which(newEdge[,1] ==0)
#tips: make them 1:(#tips)
#tips should be in edge matrix once:
whEdgeTips<-match(newTips,newEdge) #find edges that contain tips
consecutiveTips<-match(newTips,sort(newTips)) #give them consecutive numbers in same order as previous
newEdge[whEdgeTips]<-consecutiveTips
whNodeTips<-match(newTips,newNodes) #this is for reordering
newNodes[whNodeTips]<-consecutiveTips
#internal nodes: make them consecutive but in same order as previously, then add root number + nTips
consecutiveNodes<-match(newNodes[-whNodeTips],sort(newNodes[-whNodeTips])) #doesn't include the 0 edge to root, so root is #1
mNodesToEdge<-match(newEdge[-whEdgeTips],newNodes[-whNodeTips]) #get one NA from 0
if(sum(is.na(mNodesToEdge))!=1) stop("coding error -- should have one na because of root")
newEdge[-whEdgeTips]<-consecutiveNodes[mNodesToEdge]+length(newTips)
newNodes[-whNodeTips]<-consecutiveNodes+length(newTips)
newEdge[whRoot,1]<-0
if(any(sort(newNodes)!=seq_along(newNodes))) stop("coding error -- did not result in consecutive node numbers")
#now need to make sure everything in right order with new edges:
newdata<-phylo4@data[nodesKeep,]
row.names(newdata)<-as.character(newNodes)
newdata<-newdata[order(newNodes),]
tipLabels<-names(newNodes)[whNodeTips]
tipLabels<-tipLabels[order(newNodes[whNodeTips])]
nodeLabels<-names(newNodes)[-whNodeTips]
nodeLabels<-nodeLabels[order(newNodes[-whNodeTips])]
##edge length slots: edge, edge.length, edge.label
##node length slots: data (rows), label
##Don't change: order, metadata, annote
return(phylobase::phylo4d(x=newEdge,
edge.length = phylo4@edge.length[whEdgesKeep],
tip.label = tipLabels,
node.label = nodeLabels,
edge.label = phylo4@edge.label[whEdgesKeep],
order = phylo4@order,
annote = phylo4@annote,
all.data=newdata,
metadata=phylo4@metadata)
)
}
.safePhyloSubset<-function(phylo4,tipsRemove,nodeName){
if(length(phylobase::tipLabels(phylo4))-length(tipsRemove)<2){
###Check that would have >1 tips left after remove (otherwise gives an error, not sure why with trim.internal=FALSE; should report it)
###Remove all but 1 tip seems to work -- collapse down desptie trim.internal=FALSE. Very weird.
keptTip<-TRUE
tipKeep<-names(tipsRemove)[1] #label of the tip removed (tipsRemove has internal names as value)
tipsRemove<-tipsRemove[-1]
}
else keptTip<-FALSE
phylo4<-phylobase::subset(phylo4,tips.exclude=tipsRemove,trim.internal =FALSE)
#have to give that
if(keptTip){
labs<-phylobase::tipLabels(phylo4)
wh<-which(labs==tipKeep)
labs[wh]<-nodeName
phylobase::tipLabels(phylo4)<-labs
}
return(phylo4)
}
###Note, cluster nodes DEFINED as those whose descendants are of length>0. So edge from root of these fake binary trees needs to be > 0, and rest =0
### But also use this to make fake binary when n<5 samples and need it to stay ultrametric. Here, the edgeLength>0 will make it not ultrametric! Sigh. I fix that issue after returned (i.e. not here)
### Note that if n==1 (i.e. only 1 group), will return INVALID phylo object, because the edge matrix is matrix(NA,nrow=0,ncol=2) and Nnode=0
.makeFakeBinary<-function(tipNames,rootEdgeLength=0,edgeLength=0){
newPhylo<-list()
n<-length(tipNames)
if(n>1){
if(n>2){
newPhylo$edge<-cbind(seq(from=n+1,to=n+(n-1)-1,by=1),seq(from=n+2,to=n+(n-1),by=1))
newPhylo$edge<-rbind(newPhylo$edge,cbind(n+seq_len(n-1),seq_len(n-1)))
newPhylo$edge<-rbind(newPhylo$edge,c(n+n-1,n))
}
else if(n==2){
newPhylo$edge<-rbind(c(3,1),c(3,2))
}
newPhylo$tip.label<-tipNames
newPhylo$Nnode<-as.integer(n-1)
newPhylo$edge.length<-rep(edgeLength,length=nrow(newPhylo$edge))
whRoot<-which(newPhylo$edge==n+1,arr.ind = TRUE)
if(nrow(whRoot)>2) stop("coding error -- found more than two descendants of root")
if(any(whRoot[,"col"]==2)) stop("coding error -- found root as a descendant")
newPhylo$edge.length[whRoot[,"row"]]<-rootEdgeLength
}
else{
if(n==1){
newPhylo<-list()
newPhylo$edge<-matrix(NA,nrow=0,ncol=2)
newPhylo$tip.label<-tipNames
newPhylo$edge.length<-rootEdgeLength
newPhylo$Nnode<-as.integer(0)
}
else stop("coding error -- zero or less length tipNames")
}
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
class(newPhylo)<-"phylo"
return(newPhylo)
}
.makeIntegerMatrix<-function(mat){
#make the entries integer valued.
matrix(as.integer(mat),ncol=ncol(mat),byrow=FALSE)
}
#' @importFrom ape node.depth.edgelength
.mergePhylo<-function(tree1,tree2,mergeEdgeLength,balanceLength=TRUE){
#if balanceLength==TRUE, want to rebalance so that the two trees have same node height -- without adding to 0-length edges!
n1<-length(tree1$tip.label)
m1<-tree1$Nnode
isTree<-is.list(tree2) & is(tree2,"phylo") #whether tree2 merging is singleton or actual tree (different protocal from .addTipsToTrees...)
mergeEdgeLength1<-mergeEdgeLength2<-mergeEdgeLength
depth1<-max(ape::node.depth.edgelength(tree1))
if(isTree){
if(is.null(tree1$edge.length) || is.null(tree1$edge.length) ) stop("must have edge length on both trees")
n2<-length(tree2$tip.label)
m2<-tree2$Nnode
if(balanceLength==TRUE){
depth2<-max(ape::node.depth.edgelength(tree2))
finalDepth<-max(depth1,depth2)
if(depth1==0){
depth1<-1
mergeEdgeLength1<-finalDepth+mergeEdgeLength
}
if(depth2==0){
depth2<-1
mergeEdgeLength2<-finalDepth+mergeEdgeLength
}
tree1$edge.length<-tree1$edge.length/depth1*finalDepth
tree2$edge.length<-tree2$edge.length/depth2*finalDepth
}
}else{
if(is.null(tree1$edge.length)) stop("must have edge length to merge to tree")
if(!is.vector(tree2) || length(tree2)!=1) stop("coding error -- trying to merge add more than 1 tip to tree")
n2<-1
m2<-0
mergeEdgeLength2<-depth1+mergeEdgeLength
}
newPhylo<-list()
#1) Tree 1 inner nodes: add n2+1 (because now will have new root)
whinner1<-which(tree1$edge[,2] > n1) #including root of tree 1
if(length(whinner1)>0) tree1$edge[whinner1,2]<-tree1$edge[whinner1,2]+n2+1
tree1$edge[,1]<-tree1$edge[,1]+n2+1
#2) Number of internal nodes
newPhylo$Nnode<-m1+m2+1
#3) Rescue node labels in tree1:
#were 1:tree1$Nnode
#in edge were +n1
#moved to +n2+1 in new edge matrix
#in node index, subtract n1+n2 -> +1
newPhylo$node.label<-rep(NA,times=newPhylo$Nnode)
if(!is.null(tree1$node.label)) newPhylo$node.label[seq_len(m1)+1]<-tree1$node.label
if(isTree){
#4) Tree 2 tips: add n1
whtip2<-which(tree2$edge[,2]<=n2)
tree2$edge[whtip2,2]<-tree2$edge[whtip2,2]+n1
#5) Tree 2 inner nodes: -n2 to get to 1:... then add n2+n1+m1+1 -> +n1+m1+1
if(nrow(tree2$edge)!=length(whtip2)) tree2$edge[-whtip2,2]<-tree2$edge[-whtip2,2]+n1+m1+1
tree2$edge[,1]<-tree2$edge[,1]+n1+m1+1
#6) Add root edge (n2+n1+1) to (n1+n2+2) and (n2+m1+n2+2) to bottom of edge matrix:
newPhylo$edge<-rbind(tree1$edge,tree2$edge)
newPhylo$edge<-rbind(newPhylo$edge, rbind(c(n2+n1+1,n1+n2+2),c(n2+n1+1,n1+m1+n2+2)))
#7) tip.label
newPhylo$tip.label<-c(tree1$tip.label,tree2$tip.label)
#8) #should there be check that there is edge length?
newPhylo$edge.length<-c(tree1$edge.length,tree2$edge.length,c(mergeEdgeLength1,mergeEdgeLength2))
#9) Rescue node labels in tree 2:
#were 1:tree2$Nnode
#in edge were +n2
#moved to +n1+m1+1 in new edge matrix
#in node index, subtract n1+n2 -> +m1+1
if(!is.null(tree2$node.label)) newPhylo$node.label[seq_len(m2)+m1+1]<-tree2$node.label
}
else{
#6) Add root edge (n2+n1+1) to tree 1 (n1+n2+2) and root to tip to bottom of edge matrix:
newPhylo$edge<-tree1$edge
newPhylo$edge<-rbind(newPhylo$edge, rbind(c(n2+n1+1,n1+n2+2),c(n2+n1+1,n1+n2)))
#7) tip.label: c(tree1$tip.label,tree2$tip.label)
newPhylo$tip.label<-c(tree1$tip.label,tree2)
#8)
newPhylo$edge.length<-c(tree1$edge.length,c(mergeEdgeLength1,mergeEdgeLength2))
}
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
class(newPhylo)<-"phylo"
return(newPhylo)
}
#Input:
#' @param tipTrees should be list of trees in same order as tips in mainTree
#' @param mainTree a phylo object, assumed to be rooted tree
#' @details single values to be added to tree should have $edge=0-row matrix, $Nnode=0, $tip.label name of cluster, $edge.length=value in the tipTrees list to be added to length of cluster node
#' @return
#' noRd
.addTreesToTips<-function(mainTree,tipTrees){
N<-length(mainTree$tip.label)
M<-mainTree$Nnode
if(length(tipTrees)!=N) stop("coding error -- length of list of trees must match number of tips in main Tree")
#check valid phylo objects
isPhylo<-sapply(tipTrees,class)=="phylo"
if(!all(isPhylo)) stop("coding error -- each of the new trees must be of class phylo")
# check<-sapply(tipTrees,.testPhyloObject,verbose=FALSE)
# check<-.testPhyloObject(mainTree)
nVec<-sapply(tipTrees,function(x){length(x$tip.label)})
mVec<-sapply(tipTrees,function(x){x$Nnode})
isSingle<-sapply(tipTrees,function(x){nrow(x$edge)==0})
cumN<-c(0,cumsum(nVec))
cumM<-c(0,cumsum(pmax(mVec-1,0))) #cumulative number of NON-ROOT internal
#cumSingle[i] counts how many clusters/tips on main tree were singleton before (main) tip i
cumSingle<-c(0,cumsum(as.numeric(isSingle)))
#don't need the last entry of any of these.
cumN<-head(cumN,-1)
cumM<-head(cumM,-1)
cumSingle<-head(cumSingle,-1)
##############
#change mainTree edge matrix in anticipation of adding trees to tips
##############
whRoot<-which(mainTree$edge==N+1)
whInternal<-which(mainTree$edge>N) #includes root
#1) internal nodes: add sum(nVec)-N (including root)
# note root becomes sum(nVec)+1, and the last internal edge should be sum(nVec)+M
mainTree$edge[whInternal]<-mainTree$edge[whInternal]-N+sum(nVec)
if(max(mainTree$edge[whInternal])!= sum(nVec)+M) stop("internal coding error in adding trees")
# whInternalIndex<-which(mainTree$edge>N,arr.ind=TRUE)
# whTipsIndex<-which(mainTree$edge<=N & !mainTree$edge %in% which(isSingle),arr.ind=TRUE)
#2) tips add sum(nVec)+M so now internal edges -- except those that will be continue being tip because singleton added!
whTips<-which(mainTree$edge<=N & !mainTree$edge %in% which(isSingle))
# main tree tips that are not single get consecutive numbers
mainTree$edge[whTips]<-mainTree$edge[whTips]+sum(nVec)+M-cumSingle[mainTree$edge[whTips]]
if(sum(isSingle)>0){
whSingle<-match(which(isSingle),mainTree$edge[,2])
mainTree$edge[whSingle,2]<-cumN[isSingle]+1
# Note that singletons, unlike others, short value of rootEdgeLength to their edge length, comparatively, when made with fakeBinaryTrees function. (and rootEdgeLength was added to deal with identification of cluster problem)
# Need to add to those
addValues<-sapply(tipTrees[isSingle],.subset2,"edge.length")
mainTree$edge.length[whSingle]<-mainTree$edge.length[whSingle]+addValues
}
#######
### Check valid edge matrix:
#######
# check no duplicated edges:
if(any(duplicated(mainTree$edge[,2]))) stop("internal coding error -- adding tips to tree led to duplicate edges")
newPhylo<-list()
newPhylo$Nnode<-mainTree$Nnode+sum(sapply(tipTrees,.subset2,"Nnode"))
#------
#Add back original node labels of the tree:
#------
newPhylo$node.label<-rep(NA,length=newPhylo$Nnode)
#previously internal in main were 1:mainTree$Nnode+N in edge branch;
#Moved to -N +sum(nVec)
#Then to move to nodes index by subtracting off length(newPhylo$tip.label)=sum(nVec)
#so same index...
newPhylo$node.label[seq_len(mainTree$Nnode)]<-mainTree$node.label
# main tree tips that are not single become nodes -- same formula as before
# were c(1:N)[!isSingle] in edge matrix (and tip.label)
# Then moved by +sum(nVec)+M-cumSingle[!isSingle] in edge matrix
# Then subtract of sum(nVec) to get to node index
notSingleTips<-c(seq_len(N))[!isSingle]
newPhylo$node.label[notSingleTips+M-cumSingle[!isSingle]]<-mainTree$tip.label[notSingleTips]
##############
#change treeList edgeMatrix
##############
tipTrees<-lapply(seq_along(tipTrees),function(ii){
n<-nVec[[ii]]
x<-tipTrees[[ii]]
if(nrow(x$edge)>0){
whInternal<-which(x$edge>n+1)
whRoot<-which(x$edge==n+1)
whTips<-which(x$edge<=n)
x$edge[whRoot]<-ii+sum(nVec)+M-cumSingle[ii]
# give new numbers to internal:
# 1) subtract n[i]-1 to non-root internal nodes go from 1:(m[i]-1)
# 2) + no. new tips (sum(nVec))
# 3) + no. internal of main tree (M)
# 4) + total no. tips of main that become internal (i.e. not singletons) (sum(as.numeric(!isSingle)))
# 5) + no. non-root internal of the ii-1 trees already added (cumM[ii])
x$edge[whInternal]<-x$edge[whInternal]-(n+1)+ sum(nVec) + M + sum(as.numeric(!isSingle)) + cumM[ii]
x$edge[whTips]<-x$edge[whTips]+ cumN[ii]
}
return(x)
})
newPhylo$edge<-do.call("rbind",c(lapply(tipTrees[!isSingle],.subset2,"edge"),list(mainTree$edge)))
newPhylo$tip.label<-do.call("c",lapply(tipTrees,.subset2,"tip.label"))
newPhylo$edge.length<-do.call("c",c(lapply(tipTrees[!isSingle],.subset2,"edge.length"),list(mainTree$edge.length)))
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
#singleton clusters stay tips... make sure they get the right label (namely cluster, not sample -- sort of arbitrary choice)
# were tip.label/edge values: which(isSingle)
# move to = cumN[isSingle]+1 (still tip values don't subtract off
newPhylo$tip.label[cumN[isSingle]+1]<-mainTree$tip.label[which(isSingle)]
class(newPhylo)<-"phylo"
return(newPhylo)
}
.testPhyloObject<-function(phyloObj,verbose=FALSE){
if(verbose) cat("Tests (should all be yes):\n")
.testPrint("Required elements with right name:",all(c("tip.label","edge","Nnode") %in% names(phyloObj)),verbose=verbose)
ntip<-length(phyloObj$tip.label)
ninterior<-phyloObj$Nnode
allNodes<-unique(as.numeric(phyloObj$edge))
.testPrint("Edge matrix has two columns",dim(phyloObj$edge)[2]==2,verbose=verbose)
#no gaps in series
.testPrint("No gaps", all(sort(allNodes)==seq_along(allNodes) ),verbose=verbose)
#matches expected range
.testPrint("Range of series matches expected", length(allNodes)== ntip+ninterior ,verbose=verbose)
#All elements, except the root
#n+1, appear once in the second column.
rootVal<-ntip+1
tab<-table(phyloObj$edge[,2])
.testPrint("All elements except root once in second column",all(tab[names(tab)!= as.character(rootVal)]==1),verbose=verbose)
if("edge.length" %in% names(phyloObj)){
.testPrint("edge length matches number edges",nrow(phyloObj$edge)==length(phyloObj$edge.length),verbose=verbose)
}
if(verbose){
cat("-----------\n")
cat("Number of tips:",ntip,"\n")
cat("Number of interior:",ninterior,"\n")
cat("Tips labels:",paste(phyloObj$tip.label,collapse=","),"\n")
cat("Range of edge matrix values:",paste(range(allNodes),collapse=","),"\n")
}
}
.testPrint<-function(name,logic,verbose=FALSE){
if(!is.logical(logic)) stop("logic input is not logical")
if(!verbose){
if(!logic)stop(paste("coding error -- the following check for phylo class did not pass",name))
}
else{
cat(paste0(name,":"))
if(logic) cat("Yes\n") else cat("No\n")
}
}
.force.ultrametric<-function(tree){
##From http://blog.phytools.org/2017/03/forceultrametric-method-for-ultrametric.html
#calculates, per tip, the amount missing and adds it to the tips.
if(inherits(tree,"phylo")){
depth<-ape::node.depth.edgelength(tree) #in order of all nodes
ntips<-length(tree$tip.label)
maxD<-max(depth[seq_len(ntips)])
addValue<-maxD-depth[seq_len(ntips)]
whTips<-match(seq_len(ntips),tree$edge[,2])
tree$edge.length[whTips]<-tree$edge.length[whTips]+addValue
return(tree)
}
else if(!inherits(tree,"phylo4")){
stop("tree must be of class phylo4")
} else{
allTips<-phylobase::tipLabels(tree)
depthToTips<-phylobase::nodeHeight(tree,allTips,from="root")
maxD<-max(depthToTips)
addValue<-maxD-depthToTips
allLen<-phylobase::edgeLength(tree)
edgeMat<-phylobase::edges(tree)
#add 'addValue' to the tips so ultrametric
tipIds<-as.numeric(names(allTips))
m<-match(tipIds,edgeMat[,2])
edgeIds<-paste(edgeMat[m,1],edgeMat[m,2],sep="-")
#check didn't do something stupid:
checkTipEdges<-phylobase::edgeId(tree,type="tip")
if(!identical(sort(unname(checkTipEdges)),sort(unname(edgeIds)))) stop("coding error -- didn't correctly get edge ids for tips")
#replace with new edges:
allLen[edgeIds]<-allLen[edgeIds]+addValue
phylobase::edgeLength(tree)<-allLen
return(tree) #returns phylo4 tree
}
}
# #---------
# #old code that made non-binary tree by hand.
# #---------
# tab<-table(cl[whPos])
# newPhylo<-list()
#
# if(any(tab==1)){
# cluster1<-names(tab)[tab==1]
# nCluster1<-length(cluster1)
# mClToTip1<-match(cluster1,phyloObj$tip.label) #find their tip number in matrix
# tipEdges1<-phyloObj$edge[phyloObj$edge[,2]==mClToTip1, ,drop=FALSE] #get the edge matrix for them
# mToPositiveCl<-match(tipEdges1[,2],cl[whPos])
# tipEdges1[,2]<-mToPositiveCl #change their tip number to their index in positive cluster vector
#
# }
# else{
# nCluster1<-0
# tipEdges1<-matrix(0,nrow=0,ncol=2)
# }
# if(any(tab>1)){
# clusterGr1<-names(tab)[tab>1]
# mGr1<-which(as.character(cl[whPos]) %in% clusterGr1)
# newPhylo$edge<-cbind(cl[whPos][mGr1],mGr1)
#
# mClToTip<-match(as.character(newPhylo$edge[,1]),phyloObj$tip.label) #gives for each cluster, tip number in old cluster tree
# if(any(is.na(mClToTip))) stop("coding error -- some of tip labels in phylo object do not match cluster names")
# newPhylo$edge[,1]<-mClToTip
# newPhylo$edge<-rbind(newPhylo$edge,tipEdges1)
# }
# #---------
# ##Some tests -- might drop them for speed later
# #---------
# if(any(newPhylo$edge[,2]>length(cl[whPos]))) stop("coding error -- gave tip values greater than number of assigned samples")
# if(nrow(newPhylo$edge)!=length(cl[whPos])) stop("coding error -- did not assign all assigned samples to tip of tree")
# if(length(newPhylo$edge[,2])!=length(unique(newPhylo$edge[,2]))) stop("coding error -- did not give unique ids to tips of tree")
#
# #-------
# #make tips have values larger than root
# #-------
# internalEdges<-phyloObj$edge
# nOrigTips<-length(phyloObj$tip.label)
# maxOrig<-nOrigTips+phyloObj$Nnode
# whTipInternal<-internalEdges[,2]<=nOrigTips
# internalEdges[whTipInternal,2]<-internalEdges[whTipInternal,2]+maxOrig
# #fix up the newPhylo ones to have same number (again, for speed if fix to begin with?)
# whTipNew<-newPhylo$edge[,1]<=nOrigTips
# newPhylo$edge[whTipNew,1]<-newPhylo$edge[whTipNew,1]+maxOrig
#
#
# if(any(tab==1)){
# #have to remove those edges that went to clusters of size 1, because won't be internal edges.
# internalEdges<-internalEdges[ phyloObj$edge[,2]!=mClToTip1, ,drop=FALSE]
# }
# #also need to renumber everything, because the tip lost will leave gap... Need to keep the same order.
# oldValues<-sort( unique( as.numeric( internalEdges )))
# newValues<-1:length(oldValues)
# m1<-match(internalEdges[,1],oldValues)
# m2<-match(internalEdges[,2],oldValues)
# internalEdges<-cbind(newValues[m1],newValues[m2])
#
# #now fix up the edge matrix too; speed wise, is it faster to do it before? More complicated to code it before...
# newPhylo$edge[,1]<-newValues[match(newPhylo$edge[,1],oldValues)]
# internalEdges<-internalEdges+length(cl[whPos])
# newPhylo$edge[,1]<-newPhylo$edge[,1]+length(cl[whPos])
# newPhylo$edge<-rbind(internalEdges,newPhylo$edge)
#
# if(!is.null(sampleNames)) newPhylo$tip.label<-sampleNames[whPos]
# else{
# newPhylo$tip.label<-paste("Sample",whPos)
# }
# newPhylo$Nnode<-phyloObj$Nnode+length(phyloObj$tip.label)-nCluster1
# if("edge.length" %in% names(phyloObj)){
# oldEdgeLength<-phyloObj$edge.length
# if( any(tab==1) ) oldEdgeLength<-oldEdgeLength[phyloObj$edge[,2]!=mClToTip1]
# newPhylo$edge.length<-rep(sampleEdgeLength,length=length(newPhylo$tip.label))
# if(any(tab==1)){ #need get back length to single-sample cluster
# oldEdgeLength1<-phyloObj$edge.length[phyloObj$edge[,2]==mClToTip1]
# newPhylo$edge.length[(length(newPhylo$edge.length)-nCluster1+1):length(newPhylo$edge.length)]<-oldEdgeLength1
# }
# newPhylo$edge.length<-c(oldEdgeLength,newPhylo$edge.length)
# }
# class(newPhylo)<-"phylo"
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Defines functions .force.ultrametric .testPrint .testPhyloObject .addTreesToTips .mergePhylo .makeIntegerMatrix .makeFakeBinary .safePhyloSubset .pruneToNodes .convertToPhyClasses .setNodeLabels .getClusterIds .matchToDendroData .hasOutBranch .makeSampleNames
.makeSampleNames<-function(x){paste("Sample",as.character(x))}
.clusterDendroColumns<-c("Position","ClusterIdDendro","ClusterIdMerge","NodeId")
.clusterSampleColumns<-c("Position","NodeId","SampleIndex")
.positionLevels<-c("cluster hierarchy node","cluster hierarchy tip","tip hierarchy","assigned tip","outbranch hierarchy node","unassigned tip","outbranch root")
.hasOutBranch<-function(object){
"outbranch root" %in% phylobase::tdata(object@dendro_samples)$Position
}
#' @description internal functions used by the package to manipulate dendrograms
#' @param inputValue a vector of values to match to dendro data
#' @param dendro a phylo4d object
#' @param matchColumn a character value giving the name of a column in the \code{tdata} of the dendro to match to. If "NodeIndex", means that will match to the row number (i.e. inputValue is a integer giving the row index); in this case it is the same as doing tdata(dendro)[inputValue,returnColumn]
#' @param returnColumn a character value giving the name of a column to return -- i.e. after matching to the matchColumn, return the corresponding values in the returnColumn. If returnColumn="NodeIndex", then just the index of the match is returned.
#' @noRd
.matchToDendroData<-function(inputValue,dendro,matchColumn="NodeId",returnColumn){
#Note that matchColumn="NodeIndex" means inputs give rows of the df. returnColumn="NodeIndex" means to return the index that matches (i.e. nodeIndex too)
df<-phylobase::tdata(dendro,type="all")
if(!is.character(returnColumn) || !is.character(matchColumn)) stop("coding error -- returnColumn and matchColumn must be character valued")
if(!returnColumn=="NodeIndex" && !returnColumn %in% names(df)) stop("coding error -- invalid value of returnColumn ")
if(!matchColumn=="NodeIndex" && !matchColumn %in% names(df)) stop("coding error -- invalid value of matchColumn")
if(!matchColumn=="NodeIndex") m<-match(inputValue, df[,matchColumn]) else m<-inputValue
if(any(is.na(m))) stop("coding error -- invalid value in inputValue (not in dendro)")
if(returnColumn=="NodeIndex") return(m)
else return(df[m,returnColumn])
}
.getClusterIds<-function(tipIndex,clusterDendro,returnValue=c("ClusterIdDendro","ClusterIdMerge")){
returnValue<-match.arg(returnValue)
tipNames <- .matchToDendroData(tipIndex,clusterDendro,matchColumn="NodeIndex",returnColumn=returnValue)
tipNames<-gsub("ClusterId","",as.character(tipNames))
return(tipNames)
}
#' @description phylo4d objects for cluster and sample dendrograms with pretty (and matched!) node and tip labels.
#' @param object a ClusterExperiment object
#' @param labelType. If 'id' returns the NodeId value for all the internal nodes that match the cluster dendrogram (cluster and sample dendrograms) and the cluster id for the tips (cluster dendrogram) or sample index for the tips (sample dendrogram). If "name", then the cluster ids and sample indices are converted into the cluster names (in the clusterMat) and the sample names (in colnames)
#' @param useMergeClusters if TRUE and there is an active merge, will remove the dendrogram cluster ids, and instead use merge cluster ids (which means will nave no label for dendrogram cluster merged)
#' @return Returns list of the two dendrograms with nodes that have been updated with names 'dendro_clusters' and 'dendro_samples'. Note they do not match requirement of the clusterExperiment object because have labels for nodes they "shouldn't".
#' @details Different from convertToPhyClasses, which is trying to get the needed info into the phylo or phylo4 class that doesn't have tdata. Calls that function internally
#' @noRd
.setNodeLabels<-function(object,labelType=c("name","id"),useMergeClusters=FALSE,overrideExistingNode=FALSE,singletonCluster=c("sample","cluster"),...){
labelType<-match.arg(labelType)
singletonCluster<-match.arg(singletonCluster)
if(!inherits(object,"ClusterExperiment")) stop("coding error -- function should be used for ClusterExperiment objects")
if(is.na(object@merge_index)|| all(is.na(phylobase::tdata(object@dendro_clusters)$ClusterIdMerge))) useMergeClusters<-FALSE
if(is.null(object@dendro_clusters)) return(NULL)
#internal option returns same as the .convertPhyClasses with both =TRUE
internalCluster<-.convertToPhyClasses(object@dendro_clusters, returnClass=c("phylo4d"), convertNodes=TRUE, convertTips=TRUE)
internalSamples<-.convertToPhyClasses(object@dendro_samples, returnClass=c("phylo4d"), convertNodes=TRUE, convertTips=TRUE)
if(useMergeClusters){
#erase all the dendro cluster Ids, which are only on the tips
whConvert<-which(!is.na(phylobase::tdata(internalCluster,type="tip")$ClusterIdDendro))
phylobase::tipLabels(internalCluster)[whConvert]<-NA
#now add merge cluster ids.
whConvert<-which(!is.na(phylobase::tdata(internalCluster,type="all")$ClusterIdMerge))
phylobase::labels(internalCluster)[whConvert] <- phylobase::tdata(internalCluster,type="all")$ClusterIdMerge[whConvert]
}
if(!overrideExistingNode){
#located here so merge labels won't be displayed if user changed that node name manually.
existingNodeLabels<-phylobase::nodeLabels(object@dendro_clusters)
whKeep<-which(!is.na(existingNodeLabels) & existingNodeLabels!=phylobase::tdata(internalCluster,type="internal")$NodeId)
phylobase::nodeLabels(internalCluster)[whKeep]<-existingNodeLabels[whKeep]
}
if(labelType=="name"){
###Convert to the name versions
if(useMergeClusters){
legMat<-clusterLegend(object)[[object@merge_index]]
labs<-phylobase::labels(internalCluster)[whConvert]
labs<-as.character(as.numeric(gsub("ClusterId","",labs)))
m<-match(labs,legMat[,"clusterIds"])
phylobase::labels(internalCluster)[whConvert]<-legMat[m,"name"]
}
else{
legMat<-clusterLegend(object)[[object@dendro_index]]
labs<-phylobase::tipLabels(internalCluster)
labs<-as.character(as.numeric(gsub("ClusterId","",labs)))
m<-match(labs,legMat[,"clusterIds"])
phylobase::tipLabels(internalCluster)<-legMat[m,"name"]
}
nms<-if(!is.null(colnames(object))) colnames(object) else .makeSampleNames(seq_len(ncol(object)))
phylobase::tipLabels(internalSamples) <- nms[as.numeric(phylobase::tipLabels(internalSamples))]
}
#Make sample node names match
type<-switch(singletonCluster,"sample"="internal","cluster"="all")
vals<-phylobase::tdata(internalSamples,type=type)$NodeId
wh<-which(!is.na(vals))
mToSample <- .matchToDendroData(inputValue=vals[wh], dendro=internalCluster, matchColumn="NodeId", returnColumn="NodeIndex")
phylobase::labels(internalSamples,type=type)[wh]<- phylobase::labels(internalCluster)[mToSample]
return(list(dendro_clusters=internalCluster,dendro_samples=internalSamples))
}
#' @param convertNodes logical. If true, the returned dendrogram will have the node labels change to be NodeId
#' @param convertTips logical. If true, the returned dendrogram will have the tip labels changed. If 'ClusterIdDendro' is in tdata (i.e. its a cluster dendrogram) then they are converted to Dendro cluster id (if no NAs) or if there are NAs, then merge cluster id (if dendros are NA in tips). If 'SampleIndex' is column name in tdata (i.e. is a samples dendrogram), then returns tip labels that are the SampleIndex value
#' @importFrom stats as.hclust
#' @importFrom ape as.phylo.hclust
#' @details phylo is class in ape package (S3). phylo4 and phylo4d are classes from phylobase package -- S4 version of phylo.
#' @noRd
.convertToPhyClasses<-function(x,returnClass=c("phylo4","phylo","phylo4d"),convertNodes=FALSE,convertTips=FALSE){
returnClass<-match.arg(returnClass)
if(inherits(x,"phylo4d") ){
if(returnClass %in% c("phylo","phylo4","phylo4d")){
#------
#Before convert,
#make internal node and cluster ids
#the node and tip labels (i.e. erase existing)
#------
if(convertNodes)
phylobase::nodeLabels(x)<-as.character(
phylobase::tdata(x,type="internal")$NodeId)
if(convertTips){
if("ClusterIdDendro" %in%
names(phylobase::tdata(x,type="all"))){
phylobase::tipLabels(x)<-as.character(
phylobase::tdata(x,type="tip")$ClusterIdDendro)
if(any(is.na(phylobase::tipLabels(x)))){
#this should mean its the cluster dendrogram limited to the merge ids.
phylobase::tipLabels(x)<-as.character(phylobase::tdata(x,type="tip")$ClusterIdMerge)
}
if(any(is.na(phylobase::tipLabels(x)))) stop("coding error -- even after accounting for merge id, still have NA values")
}
else if("SampleIndex" %in% names(phylobase::tdata(x,type="all")))
phylobase::tipLabels(x)<-as.character(phylobase::tdata(x,type="tip")$SampleIndex)
else stop("coding error -- tree should have either 'ClusterIdDendro' or 'SampleIndex' as names in tdata(x)")
}
}
if(returnClass %in% c("phylo4","phylo4d")) return(x)
}
if(!inherits(x,"phylo4d") & returnClass=="phylo4d") stop("coding error -- can't convert other classes to phylo4d at this time and still retain all correct information")
if(inherits(x,"dendrogram")){
x<-try(stats::as.hclust(x),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from dendrogram to hclust object. Reported error:",x)
}
if(inherits(x,"hclust")){
x<-try(ape::as.phylo.hclust(x),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from hclust to phylo object. Reported error:",x)
}
if(inherits(x,"phylo")){
if(returnClass=="phylo") return(x)
else{
## FIXME: getting warning here in test of plotCoClustering
## Commented out test for now, need to go back to it.
x<-try(as(x,"phylo4"),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from phylo to phylo4 object. Reported error:",x)
return(x)
}
}
if(inherits(x,"phylo4")){
if(returnClass=="phylo4") return(x)
else{
#phylobase warnings that trees with unknown edge order may be unsafe. This is probably because of this problem they ran into: http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2009-January/000353.html
#but the problem has probably been fixed by now in ape!
x<-try(suppressWarnings(as(x,"phylo")),TRUE)
if(inherits(x, "try-error")) stop("coding error -- could not convert from phylo4 to phylo object. Reported error:",x)
#checkValidPhylo(x) returns NULL whether true or not.
return(x)
}
}
else{ stop("input x is not of hclust, dendrogram, phylo or phylo4 class")}
}
.pruneToNodes<-function(phylo4,nodesPruned){
##nodesPruned should be *the node numerical index* of those nodes that need "pruning" -- i.e. drop their children; other nodes kept the same.
tipsPruned<-unlist(phylobase::descendants(phylo4,node=nodesPruned,type="tip"),use.names=FALSE)
tipsKept<-phylobase::getNode(phylo4,type="tip")
tipsKept<-tipsKept[!tipsKept %in% tipsPruned]
nodesKeep<-c(nodesPruned,tipsKept)
allNodes<-phylobase::getNode(phylo4,type="all")
if(!all(nodesKeep %in% allNodes))
stop("nodes specified are not valid")
nodesKeep<-unique(unlist(phylobase::ancestors(phylo4,nodesKeep,"ALL"),use.names=FALSE)) #ALL means include self
names(nodesKeep)<-names(allNodes)[nodesKeep]
whEdgesKeep<-which(phylobase::edges(phylo4)[,2] %in% nodesKeep)
newEdge<-phylobase::edges(phylo4)[whEdgesKeep,]
#need to get rid of singleton nodes -- i.e. nodes with only 1 descendant
#this won't happen I think in my merge tree example, so make it error...
singletonNode<-if(length(which(table(newEdge[-which(newEdge[,1]==0),1])==1))>0) stop("coding error -- removing these nodes creates internal nodes that are singletons. Should be only choice of nodes that 'prunes' back the tree, not actually subsetting.")
#----------
#have to renumber everything so consecutive... technically documentation doesn't say that, but actually do (error otherwise)
#----------
#get the current numbers of tips, internal nodes, and root
#this is so know how to match the names, etc. back to them
newTips<-newEdge[which(!newEdge[,2] %in% newEdge[,1]),2]
newNodes<-nodesKeep
root<-newEdge[newEdge[,1] ==0,2]
whRoot<-which(newEdge[,1] ==0)
#tips: make them 1:(#tips)
#tips should be in edge matrix once:
whEdgeTips<-match(newTips,newEdge) #find edges that contain tips
consecutiveTips<-match(newTips,sort(newTips)) #give them consecutive numbers in same order as previous
newEdge[whEdgeTips]<-consecutiveTips
whNodeTips<-match(newTips,newNodes) #this is for reordering
newNodes[whNodeTips]<-consecutiveTips
#internal nodes: make them consecutive but in same order as previously, then add root number + nTips
consecutiveNodes<-match(newNodes[-whNodeTips],sort(newNodes[-whNodeTips])) #doesn't include the 0 edge to root, so root is #1
mNodesToEdge<-match(newEdge[-whEdgeTips],newNodes[-whNodeTips]) #get one NA from 0
if(sum(is.na(mNodesToEdge))!=1) stop("coding error -- should have one na because of root")
newEdge[-whEdgeTips]<-consecutiveNodes[mNodesToEdge]+length(newTips)
newNodes[-whNodeTips]<-consecutiveNodes+length(newTips)
newEdge[whRoot,1]<-0
if(any(sort(newNodes)!=seq_along(newNodes))) stop("coding error -- did not result in consecutive node numbers")
#now need to make sure everything in right order with new edges:
newdata<-phylo4@data[nodesKeep,]
row.names(newdata)<-as.character(newNodes)
newdata<-newdata[order(newNodes),]
tipLabels<-names(newNodes)[whNodeTips]
tipLabels<-tipLabels[order(newNodes[whNodeTips])]
nodeLabels<-names(newNodes)[-whNodeTips]
nodeLabels<-nodeLabels[order(newNodes[-whNodeTips])]
##edge length slots: edge, edge.length, edge.label
##node length slots: data (rows), label
##Don't change: order, metadata, annote
return(phylobase::phylo4d(x=newEdge,
edge.length = phylo4@edge.length[whEdgesKeep],
tip.label = tipLabels,
node.label = nodeLabels,
edge.label = phylo4@edge.label[whEdgesKeep],
order = phylo4@order,
annote = phylo4@annote,
all.data=newdata,
metadata=phylo4@metadata)
)
}
.safePhyloSubset<-function(phylo4,tipsRemove,nodeName){
if(length(phylobase::tipLabels(phylo4))-length(tipsRemove)<2){
###Check that would have >1 tips left after remove (otherwise gives an error, not sure why with trim.internal=FALSE; should report it)
###Remove all but 1 tip seems to work -- collapse down desptie trim.internal=FALSE. Very weird.
keptTip<-TRUE
tipKeep<-names(tipsRemove)[1] #label of the tip removed (tipsRemove has internal names as value)
tipsRemove<-tipsRemove[-1]
}
else keptTip<-FALSE
phylo4<-phylobase::subset(phylo4,tips.exclude=tipsRemove,trim.internal =FALSE)
#have to give that
if(keptTip){
labs<-phylobase::tipLabels(phylo4)
wh<-which(labs==tipKeep)
labs[wh]<-nodeName
phylobase::tipLabels(phylo4)<-labs
}
return(phylo4)
}
###Note, cluster nodes DEFINED as those whose descendants are of length>0. So edge from root of these fake binary trees needs to be > 0, and rest =0
### But also use this to make fake binary when n<5 samples and need it to stay ultrametric. Here, the edgeLength>0 will make it not ultrametric! Sigh. I fix that issue after returned (i.e. not here)
### Note that if n==1 (i.e. only 1 group), will return INVALID phylo object, because the edge matrix is matrix(NA,nrow=0,ncol=2) and Nnode=0
.makeFakeBinary<-function(tipNames,rootEdgeLength=0,edgeLength=0){
newPhylo<-list()
n<-length(tipNames)
if(n>1){
if(n>2){
newPhylo$edge<-cbind(seq(from=n+1,to=n+(n-1)-1,by=1),seq(from=n+2,to=n+(n-1),by=1))
newPhylo$edge<-rbind(newPhylo$edge,cbind(n+seq_len(n-1),seq_len(n-1)))
newPhylo$edge<-rbind(newPhylo$edge,c(n+n-1,n))
}
else if(n==2){
newPhylo$edge<-rbind(c(3,1),c(3,2))
}
newPhylo$tip.label<-tipNames
newPhylo$Nnode<-as.integer(n-1)
newPhylo$edge.length<-rep(edgeLength,length=nrow(newPhylo$edge))
whRoot<-which(newPhylo$edge==n+1,arr.ind = TRUE)
if(nrow(whRoot)>2) stop("coding error -- found more than two descendants of root")
if(any(whRoot[,"col"]==2)) stop("coding error -- found root as a descendant")
newPhylo$edge.length[whRoot[,"row"]]<-rootEdgeLength
}
else{
if(n==1){
newPhylo<-list()
newPhylo$edge<-matrix(NA,nrow=0,ncol=2)
newPhylo$tip.label<-tipNames
newPhylo$edge.length<-rootEdgeLength
newPhylo$Nnode<-as.integer(0)
}
else stop("coding error -- zero or less length tipNames")
}
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
class(newPhylo)<-"phylo"
return(newPhylo)
}
.makeIntegerMatrix<-function(mat){
#make the entries integer valued.
matrix(as.integer(mat),ncol=ncol(mat),byrow=FALSE)
}
#' @importFrom ape node.depth.edgelength
.mergePhylo<-function(tree1,tree2,mergeEdgeLength,balanceLength=TRUE){
#if balanceLength==TRUE, want to rebalance so that the two trees have same node height -- without adding to 0-length edges!
n1<-length(tree1$tip.label)
m1<-tree1$Nnode
isTree<-is.list(tree2) & is(tree2,"phylo") #whether tree2 merging is singleton or actual tree (different protocal from .addTipsToTrees...)
mergeEdgeLength1<-mergeEdgeLength2<-mergeEdgeLength
depth1<-max(ape::node.depth.edgelength(tree1))
if(isTree){
if(is.null(tree1$edge.length) || is.null(tree1$edge.length) ) stop("must have edge length on both trees")
n2<-length(tree2$tip.label)
m2<-tree2$Nnode
if(balanceLength==TRUE){
depth2<-max(ape::node.depth.edgelength(tree2))
finalDepth<-max(depth1,depth2)
if(depth1==0){
depth1<-1
mergeEdgeLength1<-finalDepth+mergeEdgeLength
}
if(depth2==0){
depth2<-1
mergeEdgeLength2<-finalDepth+mergeEdgeLength
}
tree1$edge.length<-tree1$edge.length/depth1*finalDepth
tree2$edge.length<-tree2$edge.length/depth2*finalDepth
}
}else{
if(is.null(tree1$edge.length)) stop("must have edge length to merge to tree")
if(!is.vector(tree2) || length(tree2)!=1) stop("coding error -- trying to merge add more than 1 tip to tree")
n2<-1
m2<-0
mergeEdgeLength2<-depth1+mergeEdgeLength
}
newPhylo<-list()
#1) Tree 1 inner nodes: add n2+1 (because now will have new root)
whinner1<-which(tree1$edge[,2] > n1) #including root of tree 1
if(length(whinner1)>0) tree1$edge[whinner1,2]<-tree1$edge[whinner1,2]+n2+1
tree1$edge[,1]<-tree1$edge[,1]+n2+1
#2) Number of internal nodes
newPhylo$Nnode<-m1+m2+1
#3) Rescue node labels in tree1:
#were 1:tree1$Nnode
#in edge were +n1
#moved to +n2+1 in new edge matrix
#in node index, subtract n1+n2 -> +1
newPhylo$node.label<-rep(NA,times=newPhylo$Nnode)
if(!is.null(tree1$node.label)) newPhylo$node.label[seq_len(m1)+1]<-tree1$node.label
if(isTree){
#4) Tree 2 tips: add n1
whtip2<-which(tree2$edge[,2]<=n2)
tree2$edge[whtip2,2]<-tree2$edge[whtip2,2]+n1
#5) Tree 2 inner nodes: -n2 to get to 1:... then add n2+n1+m1+1 -> +n1+m1+1
if(nrow(tree2$edge)!=length(whtip2)) tree2$edge[-whtip2,2]<-tree2$edge[-whtip2,2]+n1+m1+1
tree2$edge[,1]<-tree2$edge[,1]+n1+m1+1
#6) Add root edge (n2+n1+1) to (n1+n2+2) and (n2+m1+n2+2) to bottom of edge matrix:
newPhylo$edge<-rbind(tree1$edge,tree2$edge)
newPhylo$edge<-rbind(newPhylo$edge, rbind(c(n2+n1+1,n1+n2+2),c(n2+n1+1,n1+m1+n2+2)))
#7) tip.label
newPhylo$tip.label<-c(tree1$tip.label,tree2$tip.label)
#8) #should there be check that there is edge length?
newPhylo$edge.length<-c(tree1$edge.length,tree2$edge.length,c(mergeEdgeLength1,mergeEdgeLength2))
#9) Rescue node labels in tree 2:
#were 1:tree2$Nnode
#in edge were +n2
#moved to +n1+m1+1 in new edge matrix
#in node index, subtract n1+n2 -> +m1+1
if(!is.null(tree2$node.label)) newPhylo$node.label[seq_len(m2)+m1+1]<-tree2$node.label
}
else{
#6) Add root edge (n2+n1+1) to tree 1 (n1+n2+2) and root to tip to bottom of edge matrix:
newPhylo$edge<-tree1$edge
newPhylo$edge<-rbind(newPhylo$edge, rbind(c(n2+n1+1,n1+n2+2),c(n2+n1+1,n1+n2)))
#7) tip.label: c(tree1$tip.label,tree2$tip.label)
newPhylo$tip.label<-c(tree1$tip.label,tree2)
#8)
newPhylo$edge.length<-c(tree1$edge.length,c(mergeEdgeLength1,mergeEdgeLength2))
}
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
class(newPhylo)<-"phylo"
return(newPhylo)
}
#Input:
#' @param tipTrees should be list of trees in same order as tips in mainTree
#' @param mainTree a phylo object, assumed to be rooted tree
#' @details single values to be added to tree should have $edge=0-row matrix, $Nnode=0, $tip.label name of cluster, $edge.length=value in the tipTrees list to be added to length of cluster node
#' @return
#' noRd
.addTreesToTips<-function(mainTree,tipTrees){
N<-length(mainTree$tip.label)
M<-mainTree$Nnode
if(length(tipTrees)!=N) stop("coding error -- length of list of trees must match number of tips in main Tree")
#check valid phylo objects
isPhylo<-sapply(tipTrees,class)=="phylo"
if(!all(isPhylo)) stop("coding error -- each of the new trees must be of class phylo")
# check<-sapply(tipTrees,.testPhyloObject,verbose=FALSE)
# check<-.testPhyloObject(mainTree)
nVec<-sapply(tipTrees,function(x){length(x$tip.label)})
mVec<-sapply(tipTrees,function(x){x$Nnode})
isSingle<-sapply(tipTrees,function(x){nrow(x$edge)==0})
cumN<-c(0,cumsum(nVec))
cumM<-c(0,cumsum(pmax(mVec-1,0))) #cumulative number of NON-ROOT internal
#cumSingle[i] counts how many clusters/tips on main tree were singleton before (main) tip i
cumSingle<-c(0,cumsum(as.numeric(isSingle)))
#don't need the last entry of any of these.
cumN<-head(cumN,-1)
cumM<-head(cumM,-1)
cumSingle<-head(cumSingle,-1)
##############
#change mainTree edge matrix in anticipation of adding trees to tips
##############
whRoot<-which(mainTree$edge==N+1)
whInternal<-which(mainTree$edge>N) #includes root
#1) internal nodes: add sum(nVec)-N (including root)
# note root becomes sum(nVec)+1, and the last internal edge should be sum(nVec)+M
mainTree$edge[whInternal]<-mainTree$edge[whInternal]-N+sum(nVec)
if(max(mainTree$edge[whInternal])!= sum(nVec)+M) stop("internal coding error in adding trees")
# whInternalIndex<-which(mainTree$edge>N,arr.ind=TRUE)
# whTipsIndex<-which(mainTree$edge<=N & !mainTree$edge %in% which(isSingle),arr.ind=TRUE)
#2) tips add sum(nVec)+M so now internal edges -- except those that will be continue being tip because singleton added!
whTips<-which(mainTree$edge<=N & !mainTree$edge %in% which(isSingle))
# main tree tips that are not single get consecutive numbers
mainTree$edge[whTips]<-mainTree$edge[whTips]+sum(nVec)+M-cumSingle[mainTree$edge[whTips]]
if(sum(isSingle)>0){
whSingle<-match(which(isSingle),mainTree$edge[,2])
mainTree$edge[whSingle,2]<-cumN[isSingle]+1
# Note that singletons, unlike others, short value of rootEdgeLength to their edge length, comparatively, when made with fakeBinaryTrees function. (and rootEdgeLength was added to deal with identification of cluster problem)
# Need to add to those
addValues<-sapply(tipTrees[isSingle],.subset2,"edge.length")
mainTree$edge.length[whSingle]<-mainTree$edge.length[whSingle]+addValues
}
#######
### Check valid edge matrix:
#######
# check no duplicated edges:
if(any(duplicated(mainTree$edge[,2]))) stop("internal coding error -- adding tips to tree led to duplicate edges")
newPhylo<-list()
newPhylo$Nnode<-mainTree$Nnode+sum(sapply(tipTrees,.subset2,"Nnode"))
#------
#Add back original node labels of the tree:
#------
newPhylo$node.label<-rep(NA,length=newPhylo$Nnode)
#previously internal in main were 1:mainTree$Nnode+N in edge branch;
#Moved to -N +sum(nVec)
#Then to move to nodes index by subtracting off length(newPhylo$tip.label)=sum(nVec)
#so same index...
newPhylo$node.label[seq_len(mainTree$Nnode)]<-mainTree$node.label
# main tree tips that are not single become nodes -- same formula as before
# were c(1:N)[!isSingle] in edge matrix (and tip.label)
# Then moved by +sum(nVec)+M-cumSingle[!isSingle] in edge matrix
# Then subtract of sum(nVec) to get to node index
notSingleTips<-c(seq_len(N))[!isSingle]
newPhylo$node.label[notSingleTips+M-cumSingle[!isSingle]]<-mainTree$tip.label[notSingleTips]
##############
#change treeList edgeMatrix
##############
tipTrees<-lapply(seq_along(tipTrees),function(ii){
n<-nVec[[ii]]
x<-tipTrees[[ii]]
if(nrow(x$edge)>0){
whInternal<-which(x$edge>n+1)
whRoot<-which(x$edge==n+1)
whTips<-which(x$edge<=n)
x$edge[whRoot]<-ii+sum(nVec)+M-cumSingle[ii]
# give new numbers to internal:
# 1) subtract n[i]-1 to non-root internal nodes go from 1:(m[i]-1)
# 2) + no. new tips (sum(nVec))
# 3) + no. internal of main tree (M)
# 4) + total no. tips of main that become internal (i.e. not singletons) (sum(as.numeric(!isSingle)))
# 5) + no. non-root internal of the ii-1 trees already added (cumM[ii])
x$edge[whInternal]<-x$edge[whInternal]-(n+1)+ sum(nVec) + M + sum(as.numeric(!isSingle)) + cumM[ii]
x$edge[whTips]<-x$edge[whTips]+ cumN[ii]
}
return(x)
})
newPhylo$edge<-do.call("rbind",c(lapply(tipTrees[!isSingle],.subset2,"edge"),list(mainTree$edge)))
newPhylo$tip.label<-do.call("c",lapply(tipTrees,.subset2,"tip.label"))
newPhylo$edge.length<-do.call("c",c(lapply(tipTrees[!isSingle],.subset2,"edge.length"),list(mainTree$edge.length)))
newPhylo$edge<-.makeIntegerMatrix(newPhylo$edge)
#singleton clusters stay tips... make sure they get the right label (namely cluster, not sample -- sort of arbitrary choice)
# were tip.label/edge values: which(isSingle)
# move to = cumN[isSingle]+1 (still tip values don't subtract off
newPhylo$tip.label[cumN[isSingle]+1]<-mainTree$tip.label[which(isSingle)]
class(newPhylo)<-"phylo"
return(newPhylo)
}
.testPhyloObject<-function(phyloObj,verbose=FALSE){
if(verbose) cat("Tests (should all be yes):\n")
.testPrint("Required elements with right name:",all(c("tip.label","edge","Nnode") %in% names(phyloObj)),verbose=verbose)
ntip<-length(phyloObj$tip.label)
ninterior<-phyloObj$Nnode
allNodes<-unique(as.numeric(phyloObj$edge))
.testPrint("Edge matrix has two columns",dim(phyloObj$edge)[2]==2,verbose=verbose)
#no gaps in series
.testPrint("No gaps", all(sort(allNodes)==seq_along(allNodes) ),verbose=verbose)
#matches expected range
.testPrint("Range of series matches expected", length(allNodes)== ntip+ninterior ,verbose=verbose)
#All elements, except the root
#n+1, appear once in the second column.
rootVal<-ntip+1
tab<-table(phyloObj$edge[,2])
.testPrint("All elements except root once in second column",all(tab[names(tab)!= as.character(rootVal)]==1),verbose=verbose)
if("edge.length" %in% names(phyloObj)){
.testPrint("edge length matches number edges",nrow(phyloObj$edge)==length(phyloObj$edge.length),verbose=verbose)
}
if(verbose){
cat("-----------\n")
cat("Number of tips:",ntip,"\n")
cat("Number of interior:",ninterior,"\n")
cat("Tips labels:",paste(phyloObj$tip.label,collapse=","),"\n")
cat("Range of edge matrix values:",paste(range(allNodes),collapse=","),"\n")
}
}
.testPrint<-function(name,logic,verbose=FALSE){
if(!is.logical(logic)) stop("logic input is not logical")
if(!verbose){
if(!logic)stop(paste("coding error -- the following check for phylo class did not pass",name))
}
else{
cat(paste0(name,":"))
if(logic) cat("Yes\n") else cat("No\n")
}
}
.force.ultrametric<-function(tree){
##From http://blog.phytools.org/2017/03/forceultrametric-method-for-ultrametric.html
#calculates, per tip, the amount missing and adds it to the tips.
if(inherits(tree,"phylo")){
depth<-ape::node.depth.edgelength(tree) #in order of all nodes
ntips<-length(tree$tip.label)
maxD<-max(depth[seq_len(ntips)])
addValue<-maxD-depth[seq_len(ntips)]
whTips<-match(seq_len(ntips),tree$edge[,2])
tree$edge.length[whTips]<-tree$edge.length[whTips]+addValue
return(tree)
}
else if(!inherits(tree,"phylo4")){
stop("tree must be of class phylo4")
} else{
allTips<-phylobase::tipLabels(tree)
depthToTips<-phylobase::nodeHeight(tree,allTips,from="root")
maxD<-max(depthToTips)
addValue<-maxD-depthToTips
allLen<-phylobase::edgeLength(tree)
edgeMat<-phylobase::edges(tree)
#add 'addValue' to the tips so ultrametric
tipIds<-as.numeric(names(allTips))
m<-match(tipIds,edgeMat[,2])
edgeIds<-paste(edgeMat[m,1],edgeMat[m,2],sep="-")
#check didn't do something stupid:
checkTipEdges<-phylobase::edgeId(tree,type="tip")
if(!identical(sort(unname(checkTipEdges)),sort(unname(edgeIds)))) stop("coding error -- didn't correctly get edge ids for tips")
#replace with new edges:
allLen[edgeIds]<-allLen[edgeIds]+addValue
phylobase::edgeLength(tree)<-allLen
return(tree) #returns phylo4 tree
}
}
# #---------
# #old code that made non-binary tree by hand.
# #---------
# tab<-table(cl[whPos])
# newPhylo<-list()
#
# if(any(tab==1)){
# cluster1<-names(tab)[tab==1]
# nCluster1<-length(cluster1)
# mClToTip1<-match(cluster1,phyloObj$tip.label) #find their tip number in matrix
# tipEdges1<-phyloObj$edge[phyloObj$edge[,2]==mClToTip1, ,drop=FALSE] #get the edge matrix for them
# mToPositiveCl<-match(tipEdges1[,2],cl[whPos])
# tipEdges1[,2]<-mToPositiveCl #change their tip number to their index in positive cluster vector
#
# }
# else{
# nCluster1<-0
# tipEdges1<-matrix(0,nrow=0,ncol=2)
# }
# if(any(tab>1)){
# clusterGr1<-names(tab)[tab>1]
# mGr1<-which(as.character(cl[whPos]) %in% clusterGr1)
# newPhylo$edge<-cbind(cl[whPos][mGr1],mGr1)
#
# mClToTip<-match(as.character(newPhylo$edge[,1]),phyloObj$tip.label) #gives for each cluster, tip number in old cluster tree
# if(any(is.na(mClToTip))) stop("coding error -- some of tip labels in phylo object do not match cluster names")
# newPhylo$edge[,1]<-mClToTip
# newPhylo$edge<-rbind(newPhylo$edge,tipEdges1)
# }
# #---------
# ##Some tests -- might drop them for speed later
# #---------
# if(any(newPhylo$edge[,2]>length(cl[whPos]))) stop("coding error -- gave tip values greater than number of assigned samples")
# if(nrow(newPhylo$edge)!=length(cl[whPos])) stop("coding error -- did not assign all assigned samples to tip of tree")
# if(length(newPhylo$edge[,2])!=length(unique(newPhylo$edge[,2]))) stop("coding error -- did not give unique ids to tips of tree")
#
# #-------
# #make tips have values larger than root
# #-------
# internalEdges<-phyloObj$edge
# nOrigTips<-length(phyloObj$tip.label)
# maxOrig<-nOrigTips+phyloObj$Nnode
# whTipInternal<-internalEdges[,2]<=nOrigTips
# internalEdges[whTipInternal,2]<-internalEdges[whTipInternal,2]+maxOrig
# #fix up the newPhylo ones to have same number (again, for speed if fix to begin with?)
# whTipNew<-newPhylo$edge[,1]<=nOrigTips
# newPhylo$edge[whTipNew,1]<-newPhylo$edge[whTipNew,1]+maxOrig
#
#
# if(any(tab==1)){
# #have to remove those edges that went to clusters of size 1, because won't be internal edges.
# internalEdges<-internalEdges[ phyloObj$edge[,2]!=mClToTip1, ,drop=FALSE]
# }
# #also need to renumber everything, because the tip lost will leave gap... Need to keep the same order.
# oldValues<-sort( unique( as.numeric( internalEdges )))
# newValues<-1:length(oldValues)
# m1<-match(internalEdges[,1],oldValues)
# m2<-match(internalEdges[,2],oldValues)
# internalEdges<-cbind(newValues[m1],newValues[m2])
#
# #now fix up the edge matrix too; speed wise, is it faster to do it before? More complicated to code it before...
# newPhylo$edge[,1]<-newValues[match(newPhylo$edge[,1],oldValues)]
# internalEdges<-internalEdges+length(cl[whPos])
# newPhylo$edge[,1]<-newPhylo$edge[,1]+length(cl[whPos])
# newPhylo$edge<-rbind(internalEdges,newPhylo$edge)
#
# if(!is.null(sampleNames)) newPhylo$tip.label<-sampleNames[whPos]
# else{
# newPhylo$tip.label<-paste("Sample",whPos)
# }
# newPhylo$Nnode<-phyloObj$Nnode+length(phyloObj$tip.label)-nCluster1
# if("edge.length" %in% names(phyloObj)){
# oldEdgeLength<-phyloObj$edge.length
# if( any(tab==1) ) oldEdgeLength<-oldEdgeLength[phyloObj$edge[,2]!=mClToTip1]
# newPhylo$edge.length<-rep(sampleEdgeLength,length=length(newPhylo$tip.label))
# if(any(tab==1)){ #need get back length to single-sample cluster
# oldEdgeLength1<-phyloObj$edge.length[phyloObj$edge[,2]==mClToTip1]
# newPhylo$edge.length[(length(newPhylo$edge.length)-nCluster1+1):length(newPhylo$edge.length)]<-oldEdgeLength1
# }
# newPhylo$edge.length<-c(oldEdgeLength,newPhylo$edge.length)
# }
# class(newPhylo)<-"phylo"
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