changeTree: Change the row or column tree

Description Usage Arguments Value Author(s) Examples

View source: R/changeTree.R

Description

changeTree changes a row or column tree in a TreeSummarizedExperiment object.

Usage

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changeTree(
  x,
  rowTree = NULL,
  rowNodeLab = NULL,
  colTree = NULL,
  colNodeLab = NULL,
  whichRowTree = 1,
  whichColTree = 1
)

Arguments

x

A TreeSummarizedExperiment object

rowTree

A phylo object. A new row tree.

rowNodeLab

A character string. It provides the labels of nodes that the rows of assays tables corresponding to. If NULL (default), the row names of the assays tables are used.

colTree

A phylo object. A new column tree.

colNodeLab

A character string. It provides the labels of nodes that the columns of assays tables corresponding to. If NULL (default), the column names of the assays tables are used.

whichRowTree

Which row tree to be replaced? Default is 1 (the first tree in the rowTree slot).

whichColTree

Which column tree to be replaced? Default is 1 (the first tree in the colTree slot).

Value

A TreeSummarizedExperiment object

Author(s)

Ruizhu Huang

Examples

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library(ape)
set.seed(1)
treeR <- ape::rtree(10)

# the count table
count <- matrix(rpois(160, 50), nrow = 20)
rownames(count) <- paste0("entity", 1:20)
colnames(count) <- paste("sample", 1:8, sep = "_")
# The sample information
sampC <- data.frame(condition = rep(c("control", "trt"), 
                                    each = 4),
                    gender = sample(x = 1:2, size = 8, 
                                    replace = TRUE))
rownames(sampC) <- colnames(count)
# build a TreeSummarizedExperiment object
tse <- TreeSummarizedExperiment(assays = list(count),
                                colData = sampC,
                                rowTree = treeR,
                                rowNodeLab = rep(treeR$tip.label, each =2))

treeR2 <- drop.tip(phy = treeR, tip = c("t10", "t9", "t8"))

# if rownames are not used in node labels of the tree, provide rowNodeLab
use <- changeTree(x = tse, rowTree = treeR2, 
                  rowNodeLab = rep(treeR$tip.label, each =2))
use

# if rownames are used in node labels of tree, rowNodeLab is not required.

rownames(tse) <- rep(treeR$tip.label, each =2)
cse <- changeTree(x = tse, rowTree = treeR2)
cse

fionarhuang/TreeSummarizedExperiment documentation built on June 16, 2021, 2:11 p.m.