Nothing
traverseTreeHelp <-
function(data, place, treeLvl, maxTaxaDepth, split){
REMOVELBL <- TRUE # set to false to show all labels, otherwise only non-zero labels will be shown
childStr <- ""
myName <- rownames(data)[place]
myVal <- data[place, 1]
stopTree <- FALSE
noSiblings <- TRUE
### Make sure we haven't reached our max depth yet
if(treeLvl >= maxTaxaDepth)
stopTree <- TRUE
### Find all the children from our starting point
data <- data[-place,, drop=FALSE]
childRows <- grep(paste(myName, split, sep=""), rownames(data), fixed=TRUE)
### Go through all child branches
if(length(childRows) != 0 && !stopTree){ # we know we have children
newData <- data[childRows,, drop=FALSE]
### Pull apart child branch names
rownames(newData) <- substring(rownames(newData), nchar(myName)+2, nchar(rownames(newData)))
splitLength <- unlist(lapply(strsplit(rownames(newData), split, fixed=TRUE), length))
startPlace <- which(splitLength == 1)
### Tranverse any child branches
for(t in startPlace){
temp_hstr <- traverseTreeHelp(newData, t, treeLvl+1, maxTaxaDepth, split)
if(childStr != ""){
childStr <- paste(childStr, ",", temp_hstr, sep="")
}else{
childStr <- temp_hstr
}
noSiblings <- FALSE
}
### Add child branches to our newick format to return
if(myVal == 0){ # set up string to be returned
retStr <- paste("(", childStr, "):", myVal, sep="")
}else{
retStr <- paste("(", childStr, ")", myName, ":", myVal, sep="")
}
if(noSiblings) # adds an extra 0 value branch if there are no siblings
retStr <- paste(retStr, ",:0.0", sep="")
}else{ # no children found
if(myVal == 0 && REMOVELBL == TRUE){
retStr <- paste(":", myVal, sep="")
}else{
retStr <- paste(myName, ":", myVal, sep="")
}
retStr <- paste(retStr, ",:0.0", sep="")
}
return(retStr)
}
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