Search for a target level on the tree via a specified score

Search for the target level of the tree via a specified score. The score value needs to be provided for each node of the tree.

Usage

getLevel(
  tree,
  score_data,
  drop,
  score_column,
  node_column,
  get_max,
  parent_first = TRUE,
  message = FALSE
)

Arguments

tree

A phylo object.

score_data

A data.frame providing scores for all nodes in the tree. The data frame should have at least 2 columns, one with information about nodes (the node number) and the other with the score for each node.

drop

A logical expression indicating elements or rows to keep. Missing values are taken as FALSE.

score_column

The name of the column of score_data that contains the original scores of the nodes.

node_column

The name of the column of score_data that contains the node numbers.

get_max

A logical scalar. If TRUE, search for nodes that has higher score value than its descendants; otherwise, search for nodes that has lower score value than its descendants.

parent_first

A logical scalar. If TRUE, the parent node is selected if tied values occur on the parent node and some of the children nodes.

message

A logical scalar indicating whether progress messages should be printed.

Value

A data.frame similar to score_data but with an additional column named keep indicating which nodes to retain.

Author

Ruizhu Huang

Examples

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

data(tinyTree)
ggtree(tinyTree, branch.length = "none") +
    geom_text2(aes(label = node), color = "darkblue",
           hjust = -0.5, vjust = 0.7) +
    geom_text2(aes(label = label), color = "darkorange",
               hjust = -0.1, vjust = -0.7) +
    geom_hilight(node = 13, fill = "blue", alpha = 0.3) +
    geom_hilight(node = 16, fill = "orange", alpha = 0.3)


## Generate score for each node
pv <- rep(0.1, 19)
pv[c(16, 13, 17)] <- c(0.01, 0.05, 0.005)
out <- data.frame(node = 1:19, pvalue = pv)

## Search nodes
final <- getLevel(tree = tinyTree,
                  score_data = out,
                  drop =  pvalue > 0.05,
                  score_column = "pvalue",
                  node_column = "node",
                  get_max = FALSE,
                  parent_first = TRUE,
                  message = FALSE)

## Nodes to keep
final$node[final$keep]
#> [1] 13 17