PCMTreeEvalNestedEDxOnTree | R Documentation |
Perfrorm nested extractions or drops of clades from a tree
PCMTreeEvalNestedEDxOnTree(expr, tree)
expr |
a character string representing an R expression of nested calls
of functions
|
tree |
a phylo object with named tips and internal nodes |
the resulting phylo object from evaluating expr on tree.
set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
PCMTreeSetPartRegimes(
tree, c(`26`="a", `28`="b", `45`="c", `47`="d"), setPartition = TRUE)
if(requireNamespace("ggtree"))
PCMTreePlot(
tree, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
bluePart <- PCMTreeEvalNestedEDxOnTree("D(E(tree,45),47)", tree)
PCMTreeGetPartRegimes(bluePart)
if(requireNamespace("ggtree"))
PCMTreePlot(
bluePart, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# Swapping the D and E calls has the same result:
bluePart2 <- PCMTreeEvalNestedEDxOnTree("E(D(tree,47),45)", tree)
PCMTreeGetPartRegimes(bluePart2)
if(requireNamespace("ggtree"))
PCMTreePlot(
bluePart2, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
greenPart <- PCMTreeEvalNestedEDxOnTree("E(tree,28)", tree)
bgParts <- bluePart+greenPart
if(requireNamespace("ggtree")) {
PCMTreePlot(
greenPart, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
PCMTreePlot(
bluePart + greenPart, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
PCMTreePlot(
greenPart + bluePart, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
PCMTreePlot(
bgParts, palette=c(a = "red", b = "green", c = "blue", d = "magenta")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
}
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