Nothing
##########################
### Echelon dendrogram ###
##########################
e.dendrogram<-function(peaks,locs,x,separates,c_separates,number,parents,pare_locs,progeny,
symbols,col.symbols,cex.symbols,
lwd,col,ens,adj.ens,col.ens,cex.ens,limb){
x_pos<-rep(0,times=length(peaks))
x_pos[1]<-1
if(length(peaks)!=1){
sumi<-1
k<-1
ima<-1
while(length(sumi)!=length(peaks)){
imabura<-which(parents==parents[ima])
if(all(is.element(imabura,sumi))){
ima<-parents[ima]
sumi<-c(sumi,ima)
}
else{
for(i in 1:length(imabura)){
if(!any(imabura[i]==sumi)){
ima<-imabura[i]
break
}
}
if(peaks[ima]==1){
k<-k+1
x_pos[ima]<-k
sumi<-c(sumi,ima)
}
else{
ima<-which(parents==ima)[1]
}
}
}
x_pos<-x_pos-1
}
else x_pos<--0.15
for(i in 1:length(x_pos)){
if(parents[i]==0&&progeny[i]==0){
lines(c(x_pos[i],x_pos[i]),c(x[locs[(c_separates[i]+1)]],min(x)),lwd=lwd,col=col,lty=ifelse(limb,limb[i],1))
}
else if(x_pos[i]!=-1){
lines(c(x_pos[i],x_pos[i]),c(x[locs[(c_separates[i]+1)]],x[pare_locs[i]]),lwd=lwd,col=col,lty=ifelse(limb,limb[i],1))
}
else{
if(parents[i]!=0) a<-c(x[locs[(c_separates[i]+1)]],x[pare_locs[i]])
else a<-c(x[locs[(c_separates[i]+1)]],min(x))
child<-which(parents==i)
k<-c(min(x_pos[child]),max(x_pos[child]))
lines(c(median(k),median(k)),a,lwd=lwd,col=col,lty=ifelse(limb,limb[i],1))
lines(k,c(a[1],a[1]),lwd=lwd,col=col,lty=1)
x_pos[i]<-median(k)[1]
}
}
if(!is.null(symbols)){ #symbols
temp<-NULL
for(i in 1:length(separates))
temp<-c(temp,rep(x_pos[i],times=separates[i]))
coordinate<-array(c(temp,x[locs]),dim=c(length(temp),2))
points(temp,x[locs],pch=symbols,col=col.symbols,cex=cex.symbols)
}
if(ens){ #Echelon numbers
temp<-NULL
for(i in 1:length(x_pos)) temp<-c(temp,x[locs[(c_separates[i]+1)]])
text(x_pos,temp,labels=paste("EN",number,sep=""),adj=adj.ens,col=col.ens,cex=cex.ens)
}
if(is.numeric(limb)){ ##profile legend
temp<-c("1st limb","2nd limb","3rd limb","4th limb","5th limb","6th limb-")
if(max(limb)<7) legend("bottomright",temp[1:max(limb)],lty=c(1:max(limb)))
else legend("bottomright",temp[1:6],lty=c(1:6))
}
list(coordinate=coordinate,x_pos=x_pos)
}
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