Get or set the rowTree of subsets in ExperimentSubset objects

Get the row tree of a subset: its own, if it stores one; otherwise that of the nearest subset it was made from that stores one; otherwise the main object's. TreeSummarizedExperiment's rowTree takes no subsetName, so subsets use subsetRowTree.

subsetRowTree<- stores a tree of the subset's own, linking each row to the node whose label is the row's name in the subset, without changing the main object or other subsets. Subsets made from it use the tree too, unless they store their own. NULL removes the subset's own tree. setSubsetExperiment also stores a row tree that a tool changed, but not the removal of one, as a subset always uses its own tree, a parent's or the main object's. A subset's own tree is its only row tree, so get it with whichTree = 1. rbind and cbind keep subsets' own trees; combineCols and combineRows return classes without trees (see ExperimentSubset-combine).

Usage

subsetRowTree(x, subsetName, whichTree = 1)

subsetRowTree(x, subsetName) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetRowTree(x, subsetName, whichTree = 1)

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetRowTree(x, subsetName) <- value

Arguments

x: ExperimentSubset Input ExperimentSubset object.
subsetName: character(1) Name of the subset to get the tree of, or to store it in.
whichTree: The name or position of the tree to get, as in rowTree. Default 1.
value: A phylo tree whose node labels include every rowname of the subset, or NULL.

Value

For subsetRowTree, a phylo tree, or NULL if there is none. For subsetRowTree<-, the input object with the subset's tree stored.

Examples

# a small TreeSummarizedExperiment with a tree on its rows
data("tinyTree", package = "TreeSummarizedExperiment")
counts <- matrix(1:100, nrow = 10)
rownames(counts) <- tinyTree$tip.label
tse <- TreeSummarizedExperiment(assays = list(counts = counts),
                                rowTree = tinyTree)
es <- ExperimentSubset(tse)
es <- createSubset(es, "subset1", rows = 1:5)
# the subset uses the main object's tree
subsetRowTree(es, subsetName = "subset1")
#> 
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#> 
#> Tip labels:
#>   t2, t7, t6, t9, t4, t8, ...
#> Node labels:
#>   Node_11, Node_12, Node_13, Node_14, Node_15, Node_16, ...
#> 
#> Rooted; includes branch length(s).
# store a tree with the same labels on other tips
ownTree <- tinyTree
ownTree$tip.label <- rev(tinyTree$tip.label)
subsetRowTree(es, subsetName = "subset1") <- ownTree
subsetRowLinks(es, subsetName = "subset1")
#> LinkDataFrame with 5 rows and 5 columns
#>        nodeLab   nodeNum nodeLab_alias    isLeaf   whichTree
#>    <character> <integer>   <character> <logical> <character>
#> t2          t2        10      alias_10      TRUE       phylo
#> t7          t7         9       alias_9      TRUE       phylo
#> t6          t6         8       alias_8      TRUE       phylo
#> t9          t9         7       alias_7      TRUE       phylo
#> t4          t4         6       alias_6      TRUE       phylo
# the main object's links are unchanged
rowLinks(es)[1:5, ]
#> LinkDataFrame with 5 rows and 5 columns
#>        nodeLab nodeLab_alias   nodeNum    isLeaf   whichTree
#>    <character>   <character> <integer> <logical> <character>
#> t2          t2       alias_1         1      TRUE       phylo
#> t7          t7       alias_2         2      TRUE       phylo
#> t6          t6       alias_3         3      TRUE       phylo
#> t9          t9       alias_4         4      TRUE       phylo
#> t4          t4       alias_5         5      TRUE       phylo