aggValue: Perform data aggregations based on the available tree...

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

Description

aggValue aggregates values on the leaf nodes of a tree to a specific arbitrary level of the tree. The level is specified via the nodes of the tree. Users could decide on which dimension (row or column) and how should the aggregation be performed.

Usage

aggValue(
  x,
  rowLevel = NULL,
  rowBlock = NULL,
  colLevel = NULL,
  colBlock = NULL,
  FUN = sum,
  assay = NULL,
  message = FALSE
)

Arguments

x	A TreeSummarizedExperiment object.
rowLevel	A numeric (node numbers) or character (node labels) vector. It provides the level on the tree that data is aggregated to. The aggregation is on the row dimension. The default is rowLevel = NULL, and no aggregation is performed.
rowBlock	A column name in the rowData to separate the aggregation.
colLevel	A numeric (node numbers) or character (node labels) vector. It provides the level on the tree that data is aggregated to. The aggregation is on the column dimension. The default is colLevel = NULL, and no aggregation is performed.
colBlock	A column name in the colData to separate the aggregation.
FUN	A function to be applied on the aggregation. It's similar to the FUN in apply
assay	A integer scalar or string indicating which assay of x to use in the aggregation.
message	A logical value. The default is TRUE. If TRUE, it will print out the running process.

Value

A TreeSummarizedExperiment object or a matrix. The output has the same class of the input x.

Author(s)

Ruizhu HUANG

See Also

TreeSummarizedExperiment

Examples

# assays data
set.seed(1)
toyTable <- matrix(rnbinom(20, size = 1, mu = 10), nrow = 5)
colnames(toyTable) <- paste(rep(LETTERS[1:2], each = 2),
                            rep(1:2, 2), sep = "_")
rownames(toyTable) <- paste("entity", seq_len(5), sep = "")

toyTable

# the column data
colInf <- DataFrame(gg = c(1, 2, 3, 3),
                    group = rep(LETTERS[1:2], each = 2),
                    row.names = colnames(toyTable))
colInf

# the toy tree
library(ape)
set.seed(4)
treeC <- rtree(4)
treeC$node.label <- c("All", "GroupA", "GroupB")

library(ggtree)
ggtree(treeC, size = 2) +
   geom_text2(aes(label = node), color = "darkblue",
           hjust = -0.5, vjust = 0.7, size = 6) +
    geom_text2(aes(label = label), color = "darkorange",
               hjust = -0.1, vjust = -0.7, size = 6)


tse <- TreeSummarizedExperiment(assays = list(toyTable),
                                colData = colInf,
                                colTree = treeC,
                                colNodeLab = treeC$tip.label,
                                metadata = list(test = 1:4))

aggCol <- aggValue(x = tse, colLevel = c("GroupA", "GroupB"),
FUN = sum)

assays(aggCol)[[1]]

TreeSummarizedExperiment documentation built on Dec. 8, 2020, 2 a.m.