topNodes: Generate a table of top-ranked entities (nodes)

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

Generate a table of top-ranked entities (nodes)

Description

Generate a table of top-ranked nodes from the optimal resolution candidate of entities on a tree.

Usage

topNodes(
  object,
  n = 10,
  sort_by = NULL,
  sort_decreasing = FALSE,
  sort_by_absolute = FALSE,
  p_value = 1
)

Arguments

object	An output object from evalCand.
n	An integer, the maximum number of entities to return.
sort_by	A character string specifying the column of object$output to sort by. Set to NULL to return without sorting.
sort_decreasing	A logical value indicating whether to sort by decreasing value of the sort_by column.
sort_by_absolute	A logical value indicating whether to take the absolute value of the sort_by column before sorting.
p_value	A numeric cutoff value for adjusted p-values. Only entities with adjusted p-values equal or lower than specified are returned.

Value

A data.frame with test results. The node column stores the node number for each entity.

Author(s)

Ruizhu Huang, Charlotte Soneson

Examples

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

data(tinyTree)
ggtree(tinyTree, branch.length = "none") +
   geom_text2(aes(label = node)) +
   geom_hilight(node = 13, fill = "blue", alpha = 0.3) +
   geom_hilight(node = 18, fill = "orange", alpha = 0.3)
set.seed(1)
pv <- runif(19, 0, 1)
pv[c(seq_len(5), 13, 14, 18)] <- runif(8, 0, 0.001)

fc <- sample(c(-1, 1), 19, replace = TRUE)
fc[c(seq_len(3), 13, 14)] <- 1
fc[c(4, 5, 18)] <- -1
df <- data.frame(node = seq_len(19),
                 pvalue = pv,
                 logFoldChange = fc)
ll <- getCand(tree = tinyTree, score_data = df,
               node_column = "node",
               p_column = "pvalue",
               sign_column = "logFoldChange")
cc <- evalCand(tree = tinyTree, levels = ll$candidate_list,
               score_data = df, node_column = "node",
               p_column = "pvalue", sign_column = "logFoldChange",
               limit_rej = 0.05)

## Unsorted result table
topNodes(cc)

## Sort by p-value in increasing order
topNodes(cc, sort_by = "pvalue")

fionarhuang/treeclimbR documentation built on May 19, 2024, 1:18 p.m.