# BiocManager::install("fionarhuang/TreeSummarizedExperiment")

suppressPackageStartupMessages({
    library(TreeSummarizedExperiment)
    library(ggtree)
    library(ape)})

# create a toy tree
set.seed(112)
toyTree <- ape::rtree(5)
toyTree$node.label <- LETTERS[1:4]
class(toyTree)

# plot the tree
ggtree(toyTree, size = 1.2) +
    geom_text2(aes(label = node), color = "darkblue",
               hjust = -0.5, size = 5)   +
    geom_text2(aes(label = label), color = "darkorange",
               hjust = - 2, size = 5) +
    xlim(0, 2)

# the matrix to show node numbers and node labels
leaf <- setdiff(toyTree$edge[, 2], toyTree$edge[, 1])
cbind.data.frame(nodeNum = 1:9,
                 nodeLab = c(toyTree$tip.label, toyTree$node.label))


# assays data
set.seed(1)
toyTable <- matrix(rnbinom(20, size = 1, mu = 10), nrow = 5)
colnames(toyTable) <- paste(rep(LETTERS[1:2], each = 2),
                            rep(1:2, 2), sep = "_")
rownames(toyTable) <- paste("t", seq_len(5), sep = "")
toyTable


# get children
(dd <- findOS(tree = toyTree, ancestor = "D")[[1]])
(index <- match(names(dd), rownames(toyTable)))

# get the sibling node
(ss <- findSibling(tree = toyTree, input = "C"))

# get the parent
(pp <- findAncestor(tree = toyTree, node = 9,
                    level = 1))

# get the grand parent
(gg <- findAncestor(tree = toyTree, node = 9,
                    level = 2))

# get the first share node
(hh <- shareNode(tree = toyTree, node = c(4, 5)))

# find the minumum number of nodes that cover the specified nodes
(ii <- signalNode(tree = toyTree, node = c(1, 2, 5)))

# find all paths to the root
(path <- matTree(tree = toyTree))

# Translation between node labels and node numbers
(lab <- transNode(tree = toyTree, input = 1:5))
(num <- transNode(tree = toyTree, input = lab))