Get or set the colTree of subsets in ExperimentSubset objects

Get the column 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 colTree takes no subsetName, so subsets use subsetColTree.

subsetColTree<- stores a tree of the subset's own, linking each column to the node whose label is the column'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 column 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 column 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

subsetColTree(x, subsetName, whichTree = 1)

subsetColTree(x, subsetName) <- value

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

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetColTree(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 colTree. Default 1.

value

A phylo tree whose node labels include every column name of the subset, or NULL.

Value

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

Examples

# a small TreeSummarizedExperiment with a tree on its columns
data("tinyTree", package = "TreeSummarizedExperiment")
counts <- matrix(1:100, nrow = 10)
colnames(counts) <- tinyTree$tip.label
tse <- TreeSummarizedExperiment(assays = list(counts = counts),
                                colTree = tinyTree)
es <- ExperimentSubset(tse)
es <- createSubset(es, "subset1", cols = 1:5)
# store a tree with the same labels on other tips
ownTree <- tinyTree
ownTree$tip.label <- rev(tinyTree$tip.label)
subsetColTree(es, subsetName = "subset1") <- ownTree
subsetColTree(es, subsetName = "subset1")
#> 
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#> 
#> Tip labels:
#>   t3, t5, t1, t10, t8, t4, ...
#> Node labels:
#>   Node_11, Node_12, Node_13, Node_14, Node_15, Node_16, ...
#> 
#> Rooted; includes branch length(s).
subsetColLinks(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