Extract a clade from phylogenetic tree

Extract a clade from phylogenetic tree

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

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)

Value

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

• treethe phylo object associated with the clade

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

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)
# \donttest{
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)
#>  45 
#> "c" 
# \donttest{
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")
# \donttest{
PCMTreePlot(blueTree2, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }