rename tip label by a mapping table for multiphylo tree

[neptuneyt]

Dear Dr Yu, Thanks for your such amazing work. My issue is that, Suppose I have a newick file A, and a list of old and new names mapping table B, how do I replace these names at once and keep remains still? I have try rename_taxa(tree, mapping_data, label, newlab) of treeio, but it could not support multiphylo.

• A.newick

  (a:0.2,b,c,d);
  (a:0.3,b,c,d);

• B.csv

  old,new
  a,A
  c,C
  d,D

  The result should be like:

  (A:0.2,b,C,D);
  (A:0.3,b,C,D);

  Thanks a lot!

[GuangchuangYu]

see https://yulab-smu.top/treedata-book/faq.html?q=rename#faq-modify-label.

[neptuneyt]

Thanks for your reply in time. As you mentioned, I have used rename_taxa function, but it does not support multiPhylo, and returns an error as below, I guess it used as.phylo function, but it does not support it multiPhylo obj. So do you have any good way to replace tip lables for multiPhylo object. Thanks a lot.

• demo

  > tree <- read.tree('tree.txt', keep.multi = T)  
  > write.tree(tree)
  [1] "(a:80,b:10,c:70);" "(a:80,c:70);"     
  > d <- data.frame(old = c('a','b','c'), new = c('A','B','C'))
  > rename_taxa(tree, d, old, new)
  Error in UseMethod("as.phylo") : 
  "as.phylo"没有适用于"multiPhylo"目标对象的方法

[GuangchuangYu]

you can use lapply to iterate each phylo object. The multiPhylo is just a list of phylo.