# NOT RUN {
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)
# }
# NOT RUN {
PCMTreePlot(tree, palette=c(a = "red", b = "green", c = "blue")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
redGreenTree <- PCMTreeDropClade(tree, 45)
PCMTreeGetPartRegimes(redGreenTree)
# }
# NOT RUN {
PCMTreePlot(redGreenTree, palette=c(a = "red", b = "green", c = "blue")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# we need to use the label here, because the node 29 in tree is not the same
# id in redGreenTree:
redGreenTree2 <- PCMTreeDropClade(redGreenTree, "29")
# }
# NOT RUN {
PCMTreePlot(redGreenTree2, palette=c(a = "red", b = "green", c = "blue")) +
ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
# }
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