treeScore: Generate weighted tree score accounting for the family effect

In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree

Generate weighted tree score accounting for the family effect

Description

treeScore takes the tree structure into account when calculating the score for an internal node. If an internal node A has two children B and C, (A->B, A->C), the new score at node A would be calculated as the weighted mean of the scores in the whole family (A, B and C). The weights are based on the number of descendant leaves. For example, if the node B has 2 descendant leaves, and C has 3 descendant leaves, then A would have 5. The calculation would be (Score\_A * 5 + Score\_B * 2 +Score\_C * 3)/10. The generation starts from the leaves and the new generated scores are used to update those in higher level of the tree until the root is reached.

Usage

treeScore(tree, score_data, node_column, score_column, new_score)

Arguments

tree	A phylo object.
score_data	A data frame that includes at least two columns. One column stores the number of the node, and the other stores the original score of the corresponding node.
node_column	The name of the column of score_data that contains the numbers of the nodes.
score_column	The name of the column of score_data that contains the original scores of the nodes.
new_score	The name of the column that stores the generated score.

Value

A data.frame similar to score_data, but with an extra column (named new_score) containing the weighted scores.

Author(s)

Ruizhu Huang

Examples

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

## tree
data(tinyTree)
ggtree(tinyTree, branch.length = "none") +
    geom_text2(aes(label = node))

## score
exScore <- data.frame(nodeNum = seq_len(19), score = (seq_len(19))/10)

## Calculate new score based on the tree
newScore <- treeScore(tree = tinyTree, score_data = exScore,
                      node_column = "nodeNum",
                      score_column = "score",
                      new_score = "wScore")

## Visualize the result
## The original scores are in black texts and the new ones in blue
df <- newScore |>
      rename(node = nodeNum) |>
      mutate(score = round(score, 3),
             wScore = round(wScore, 3))
ggtree(tinyTree) %<+%
   df +
   geom_text2(aes(label = score), hjust = -0.05) +
   geom_text2(aes(label = wScore, hjust = -1.2),
   color = "blue")

fionarhuang/treeclimbR documentation built on Nov. 7, 2024, 4:17 a.m.