Stack mutations to node and make branch length to number of mutation

stack_mutationTree is a naive function for stack mutation node in branch to node in a mutation tree of class "phylo".

stack_mutationTree(tre)

Arguments

tre

a mutation tree

Value

a tree of class "phylo"

Examples

library(ggtree)
#> ggtree v3.12.0 For help: https://yulab-smu.top/treedata-book/
#> 
#> If you use the ggtree package suite in published research, please cite
#> the appropriate paper(s):
#> 
#> Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
#> ggtree: an R package for visualization and annotation of phylogenetic
#> trees with their covariates and other associated data. Methods in
#> Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
#> 
#> LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
#> Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
#> for phylogenetic tree input and output with richly annotated and
#> associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.
#> doi: 10.1093/molbev/msz240
#> 
#> Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods
#> for mapping and visualizing associated data on phylogeny using ggtree.
#> Molecular Biology and Evolution. 2018, 35(12):3041-3043.
#> doi:10.1093/molbev/msy194 
nwk_text = "((((((((((8)7,(1)12)9)10)2)4)3,5,(((17)11)16)14)15)6)13)18;"
tre <- treeio::read.newick(text = nwk_text)
ggtree(tre) +
    geom_nodepoint(size = 1,color = "red",shape = 20) +
    geom_nodelab(color = "red",nudge_y = 0.1)+
    geom_nodelab(aes(label = node))+
    geom_tippoint(size = 1,color = "red",shape = 20)+
    geom_tiplab(color = "red",nudge_y = 0.1)+
    geom_tiplab(aes(label = node))

stre <- stack_mutationTree(tre)
ggtree(stre)+
  geom_nodepoint(size = 1,color = "red",shape = 20) +
  geom_nodelab(color = "red",nudge_y = 0.1,nudge_x = -0.4)+
  geom_nodelab(aes(label = node))+
  geom_tippoint(size = 1,color = "red",shape = 20)+
  geom_tiplab(color = "red",nudge_y = 0.1,nudge_x = -0.4)+
  geom_tiplab(aes(label = node))+
  theme_tree2()+
  scale_x_continuous(breaks = c(0:10), limits = c(0,12))