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) 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) 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) 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 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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