这是比较早期的文章，介绍了操作符%<%，这是我的小玩具，可以把画出来的图，当成模版，去画另一颗树。
I am very exciting that I have received very positive feedback from Ahmed Moustafa and Simon Frost.
ggtree now has equipped with a lot of new features. This time, I would like to introduce the replace operator, %<%. Suppose we have build a tree view using ggtree with multiple layers, we don’t need to run the code again to build a new tree view with another tree. In ggtree, we provides an operator, %<%, for updating tree view.
library(ggplot2)
library(ggtree)
ggtree(rtree(15)) %<% rtree(30)It supports different layout.
ggtree(rtree(15), layout="unrooted", ladderize=FALSE) %<% rtree(45)
It is chainable.
ggtree(rtree(15), layout="cladogram", ladderize=FALSE) %<%
rtree(30) %<%
rtree(45)It also supports multiple layers.
(ggtree(rtree(15), layout="fan") +
geom_point(aes(shape=isTip, color=isTip))) %<%
rtree(40)In the final example, we parse rst file from BaseML output and annotate the tree with marginal_AA_subs.
rstfile <- system.file("extdata/PAML_Baseml", "rst", package="ggtree")
tipfas <- system.file("extdata", "pa.fas", package="ggtree")
rst <- read.paml_rst(rstfile, tipfas)
p <- plot(rst, annotation="marginal_AA_subs", annotation.color="steelblue")
print(p)
We have ancestral sequences inferred from CodeML with the same tree. We can use this new data to update the tree view.
rstfile <- system.file("extdata/PAML_Codeml", "rst", package="ggtree")
rst <- read.paml_rst(rstfile, tipfas)
p %<% rst
In these two figures, we can found that they have different evolution distances, and substitutions inferred from BASEML and CODEML are slightly different.