[ggtree] updating a tree view using %<% operator

February 9, 2015
By

(This article was first published on YGC » R, and kindly contributed to R-bloggers)

I am very exciting that I have received very positive feedback from Ahmed Moustafa and Simon Frost.
Screenshot 2015-02-10 10.27.27
Screenshot 2015-02-10 10.27.07

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.

?View Code RSPLUS

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library(ggplot2)
library(ggtree)
ggtree(rtree(15)) %<% rtree(30)

Screenshot 2015-02-10 10.22.07

It supports different layout.

?View Code RSPLUS

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ggtree(rtree(15), layout="unrooted", ladderize=FALSE) %<% rtree(45)

Screenshot 2015-02-10 10.23.48

It is chainable.

?View Code RSPLUS

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ggtree(rtree(15), layout="cladogram", ladderize=FALSE) %<% 
    rtree(30) %<% 
       rtree(45)

Screenshot 2015-02-10 10.23.14

It also supports multiple layers.

?View Code RSPLUS

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(ggtree(rtree(15), layout="fan") + 
    geom_point(aes(shape=isTip, color=isTip))) %<% 
      rtree(40)

Screenshot 2015-02-10 10.25.31

In the final example, we parse rst file from BaseML output and annotate the tree with marginal_AA_subs.

?View Code RSPLUS

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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)

Screenshot 2015-02-10 10.51.17

We have ancestral sequences inferred from CodeML with the same tree. We can use this new data to update the tree view.

?View Code RSPLUS

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rstfile <- system.file("extdata/PAML_Codeml", "rst", package="ggtree")
rst <- read.paml_rst(rstfile, tipfas)
p %<% rst

Screenshot 2015-02-10 10.53.41

In these two figures, we can found that they have different evolution distances, and substitutions inferred from BASEML and CODEML are slightly different.

PS: wanna to generate a lovely heart using ggplot2, click here and here.

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