brj1
commented
2 months ago With ggdensitree you can choose the tip order. ggdensitree is for plotting multiple trees though, so it takes a list of trees.
library(ggtree)
# example tree
set.seed(0)
tree <- rtree(5)
# ggtree
ggtree(tree) + geom_tiplab()
# ggdensitree
ggdensitree(list(tree), layout = 'rectangular') + geom_tiplab()
# tip.order can be used to reorder tips
ggdensitree(list(tree), layout = 'rectangular', tip.order = paste0("t", 1:5)) + geom_tiplab()
# you can also put a more reasonable order
ggdensitree(list(tree), layout = 'rectangular', tip.order = c("t2", "t5", "t1", "t3", "t4")) + geom_tiplab()By default ggtree puts the tip labels in the order which ladderizes the tree (arranges the splits so that smaller clades go below larger clades). You can set ladderize = FALSE in ggtree's options to have it arrange tips in the order order they appear in the tree's newick file.
shenzhenzth
Dear author I have a simple question to consult, but it does confuse me. When I use ggtree, the order of tree $tip. label is always the order in the imported evolutionary tree, I discovered through reading page 128 of "R Practical" that ggtree provides a few functions for adjusting the structure called flip, If you want to adjust the order of the evolutionary tree in the specified order, can you use ggtree? In addition, I have found that the visualization results of the tree are not completely consistent with the order of the tree $tip. label. I would like to boldly ask what is the logic of this arrangement order? If you could not hesitate to give me advice, I would be extremely grateful. Wishing you a pleasant life and work A new fan of Uncle Y
亲爱的作者 我有一个简单的问题想要咨询，但是这个确实使我感到困惑。 当我使用ggtree的时候，tree$tip.label的顺序永远是导入的进化树中的顺序， 我通过阅读《R实战》128页发现了ggtree提供了少部分调整结构的函数flip， 如果想要按照指定的顺序去调整进化树的顺序，用ggtree是否能做到？ 另外我发现tree在可视化的结果中，并不完全与tree$tip.label的顺序一致，想斗胆请教一下这个排列顺序的逻辑是什么？ 如能不吝赐教、当真万分感谢。 祝您生活工作愉快 Y叔的粉丝