PCMBase (version 1.2.14)

PCMTreeExtractClade: Extract a clade from phylogenetic tree

Description

Extract a clade from phylogenetic tree

Usage

PCMTreeExtractClade(
  tree,
  cladeRootNode,
  tableAncestors = NULL,
  X = NULL,
  returnList = !is.null(X)
)

Value

If returnList is FALSE, a phylo object associated with the clade, otherwise, a list with two named members :

tree

the phylo object associated with the clade

X

the submatrix of X with columns corresponding to the tips in the clade

Arguments

tree

a PCMTree object.

cladeRootNode

a character string denoting the label or an integer denoting a node in the tree.

tableAncestors

an integer matrix returned by a previous call to PCMTreeTableAncestors(tree) or NULL.

X

an optional k x N matrix with trait value vectors for each tip in tree.

returnList

logical indicating if only the phylo object associated with the clade should be returned. Defaults to !is.null(X)

See Also

PCMTreeSpliAtNode PCMTreeDropClade

Examples

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
PCMTreeSetPartRegimes(
  tree, c(`26`="a", `28`="b", `45`="c"), setPartition = TRUE)

if(requireNamespace("ggtree"))
PCMTreePlot(tree, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)

blueTree <- PCMTreeExtractClade(tree, 45)
PCMTreeGetPartRegimes(blueTree)

if(requireNamespace("ggtree"))
PCMTreePlot(blueTree, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)

# we need to use the label here, because the node 29 in tree is not the same
# id in redGreenTree:
blueTree2 <- PCMTreeDropClade(blueTree, "48")

if(requireNamespace("ggtree"))
PCMTreePlot(blueTree2, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)