rowLinks {TreeSummarizedExperiment} | R Documentation

## TreeSummarizedExperiment-accessors

### Description

All accessor functions that work on `SingleCellExperiment` should work on TreeSummarizedExperiment. Additionally, new accessors `rowLinks` `colLinks`, `rowTree` and `colTree` accessor function are available for TreeSummarizedExperiment.

### Usage

    rowLinks(x)

    ## S4 method for signature 'TreeSummarizedExperiment'
    rowLinks(x)

    colLinks(x)

    ## S4 method for signature 'TreeSummarizedExperiment'
    colLinks(x)

    rowTree(x, whichTree = 1, value)

    ## S4 method for signature 'TreeSummarizedExperiment'
    rowTree(x, whichTree = 1, value)

    rowTree(x, whichTree = 1) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    rowTree(x, whichTree = 1) <- value

    colTree(x, whichTree = 1)

    ## S4 method for signature 'TreeSummarizedExperiment'
    colTree(x, whichTree = 1)

    colTree(x, whichTree = 1) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    colTree(x, whichTree = 1) <- value

    rowTreeNames(x, value)

    ## S4 method for signature 'TreeSummarizedExperiment'
    rowTreeNames(x, value)

    rowTreeNames(x) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    rowTreeNames(x) <- value

    colTreeNames(x, value)

    ## S4 method for signature 'TreeSummarizedExperiment'
    colTreeNames(x, value)

    colTreeNames(x) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    colTreeNames(x) <- value

    referenceSeq(x)

    ## S4 method for signature 'TreeSummarizedExperiment'
    referenceSeq(x)

    referenceSeq(x) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    referenceSeq(x) <- value

    ## S4 method for signature 'TreeSummarizedExperiment,ANY,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 replacement method for signature
    ## 'TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment'
    x[i, j, ...] <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    rownames(x) <- value

    ## S4 replacement method for signature 'TreeSummarizedExperiment'
    colnames(x) <- value

    subsetByLeaf(
      x,
      rowLeaf,
      colLeaf,
      whichRowTree,
      whichColTree,
      updateTree = TRUE
    )

    ## S4 method for signature 'TreeSummarizedExperiment'
    subsetByLeaf(
      x,
      rowLeaf,
      colLeaf,
      whichRowTree,
      whichColTree,
      updateTree = TRUE
    )

    subsetByNode(x, rowNode, colNode, whichRowTree, whichColTree)

    ## S4 method for signature 'TreeSummarizedExperiment'
    subsetByNode(x, rowNode, colNode, whichRowTree, whichColTree)

### Arguments

`x` | A TreeSummarizedExperiment object
`whichTree` | A numeric indicator or name character to specify which tree in the `rowTree` or `colTree` to be extracted. The default is to extract the first tree. If `whichTree = NULL`, a list of all trees is extracted.
`value` | the new rownames or colnames as a `character` value. See `BiocGenerics`. A `DNAStringSet` object or an object coercible to one
`i, j` | The row, column index to subset `x`. The arguments of the subset function `[]`
`...` | The argument from the subset function `[]`
`drop` | A logical value, TRUE or FALSE. The argument from the subset function `[]`
`rowLeaf` | A vector of leaves that are used to subset rows. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them.
`colLeaf` | A vector of leaves that are used to subset columns. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them.
`whichRowTree` | A numeric indicator or name character to specify which tree in the `rowTree`.
`whichColTree` | A numeric indicator or name character to specify which tree in the `colTree`.
`updateTree` | TRUE or FALSE. Default is TRUE, which updates tree structures after subsetting.
`rowNode` | A vector of nodes that are used to subset rows. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them.
`colNode` | A vector of nodes that are used to subset columns. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them.

### Value

Elements from `TreeSummarizedExperiment`.

### Author(s)

Ruizhu HUANG

### See Also

`TreeSummarizedExperiment` `SingleCellExperiment`

### Examples

    # the assay table
    set.seed(1)
    y <- matrix(rnbinom(300,size=1,mu=10),nrow=10)
    colnames(y) <- paste(rep(LETTERS[1:3], each = 10), rep(1:10,3), sep = "_")
    rownames(y) <- tinyTree$tip.label

    # the row data
    rowInf <- DataFrame(var1 = sample(letters[1:3], 10, replace = TRUE),
                        var2 = sample(c(TRUE, FALSE), 10, replace = TRUE))
    # the column data
    colInf <- DataFrame(gg = factor(sample(1:3, 30, replace = TRUE)),
                        group = rep(LETTERS[1:3], each = 10))

    # the tree structure on the rows of assay tables
    data("tinyTree")

    # the tree structure on the columns of assay tables
    sampTree <- ape::rtree(30)
    sampTree$tip.label <- colnames(y)

    # create the TreeSummarizedExperiment object
    toy_tse <- TreeSummarizedExperiment(assays = list(y),
                                        rowData = rowInf,
                                        colData = colInf,
                                        rowTree = tinyTree,
                                        colTree = sampTree)

    ## extract the rowData
    (rowD <- rowData(x = toy_tse))

    ## extract the colData
    (colD <- colData(x = toy_tse))

    ## extract the linkData
    # on rows
    (rowL <- rowLinks(x = toy_tse))
    # on columns
    (colL <- colLinks(x = toy_tse))

     ## extract the treeData
    # on rows
    (rowT <- rowTree(x = toy_tse))
    # on columns
    (colT <- colTree(x = toy_tse))

    # the referenceSeq data
    refSeq <- DNAStringSetList(one = DNAStringSet(rep("A",nrow(toy_tse))),
                               two = DNAStringSet(rep("B",nrow(toy_tse))))
    referenceSeq(toy_tse) <- refSeq
    toy_tse

    # subset treeSE by leaves
    library(ape)
    set.seed(1)
    z <- makeTSE(nrow = 5, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE)
    y <- makeTSE(nrow = 4, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE)
    tr <- ape::rtree(4)
    zy <- rbind(z, y)
    x <- changeTree(x = zy, rowTree = tr, whichRowTree = 2, rowNodeLab = tr$tip.label)
    rowLinks(zy)
    rowLinks(x)
    ## 1) rowLeaf exist only in one of trees
    rf <- c("t1", "t3")
    sx <- subsetByLeaf(x = x, rowLeaf = rf)
    rowLinks(sx)

    sx <- subsetByLeaf(x = x, rowLeaf = rf, updateTree = FALSE)
    rowLinks(sx)

    ## 2) rowLeaf exist in all trees
    rf <- 1:3
    sxx <- subsetByLeaf(x = x, rowLeaf = rf)
    rowLinks(sxx)

    ## 3) rowLeaf exist in all trees, but subset and update only the specified
    trees
    rf <- c(3:4)
    sxx <- subsetByLeaf(x = x, rowLeaf = rf, whichRowTree = "phylo")
    rowLinks(sxx)

[Package TreeSummarizedExperiment version 2.2.0 Index]