Nothing
readPhyloTree <- function(tree){
Root <- which(tree$tip.label == "NORMAL")
tree <- root(tree, Root)
result <- list()
for(i in seq_len(length(tree$edge.length)+1)){
result[[i]] <- NA
}
end <- tree$edge[which(tree$edge[,2] == Root),1]
for(i in seq_len(length(tree$tip.label))){
row <- tree$edge[which(tree$edge[,2] == i), ]
if(i == Root){
next
}
result[[i]][2] <- i
while (TRUE) {
node <- row[1]
if(node == end){
result[[node]] <- append(result[[node]], i)
break
}
else{
result[[node]] <- append(result[[node]], i)
row <- tree$edge[which(tree$edge[,2] == node),]
}
}
}
g <- lapply(result, function(x){
return(paste(sort(tree$tip.label[x[-1]], decreasing = TRUE),collapse = "&"))
})
edges_label <- unlist(g)[-Root]
nodes.num <- seq_along(tree$tip.label) - 1
tree_branch <- edges_label[order(unlist(lapply(edges_label, function(x) length(unlist(strsplit(x, split = "&"))))))]
# edges.num <- length(strsplit(tail(tree_branch, 1), split = "&")[[1]])
# tree_branch_Alias <- c(paste(rep("B", length(tree_branch)-1), (length(tree_branch)-1):1, sep = ""), "T")
tree_sampleID <- data.frame(Branch_ID = tree_branch)
return(tree_sampleID)
}
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