changeTree: Change the row or column tree

In fionarhuang/TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Description

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

Usage

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

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 Aug. 18, 2021, 12:15 p.m.