Sorting Problem of Evolutionary Leaf Node Labels//咨询进化树叶节点的排序问题

[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

[brj1]

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]

Thank you very much
I will definitely read and use the documentation carefully in the future.

Can I ask one more question?
If I want to export tree by particular "tip.order", can the demand be realized?
"write.beast" function and others seemly can not do this?

Best wishes.

[shenzhenzth]

Thank you very much
I will definitely read and use the documentation carefully in the future.

Can I ask one more question?
If I want to export tree by particular "tip.order", can the demand be realized?
"write.beast" function and others seemly can not do this?

Best wishes.