an example of drawing beast tree using ggtree

快来打我* 2022-08-05 13:11 135阅读 0赞

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

[FigTree][] is designed for viewing beast output as demonstrated by their example data:  
![Screenshot_202015-03-10_2018.15.57.png][]

BEAST output is well supported by [ ggtree][ggtree] and it's easy to reproduce such a tree view. [ ggtree][ggtree] supports parsing beast output by read.beast function. We can visualize the tree directly by using ggtree function. Since this is a time scale tree, we can set the parameter time\_scale = TRUE and ggtree will parse the time and use it as branch length.

[?][Link 1]   RSPLUS

<table> 
 <tbody> 
 <tr> 
 <td> <pre>1
2
3
4
5
6
7
8
9
10
11
12
</pre> </td> 
 <td> <pre style="font-family:monospace"><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/require.html" rel="nofollow">require</a>(ggplot2)
<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/require.html" rel="nofollow">require</a>(ggtree)
x &lt;- read.beast("/Applications/FigTree/influenza.tree")
cols &lt;- scale_color(x, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/by.html" rel="nofollow">by</a>="height")
ggtree(x, right=TRUE, time_scale=TRUE, color=cols) + theme_tree2() +
 geom_text(aes(x=<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/max.html" rel="nofollow">max</a>(x), label=label), size=1, color=cols, hjust=-.3) +
 scale_x_continuous(breaks=<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html" rel="nofollow">c</a>(1992, 1995, 1997, 2000, 2002, 2005), minor_breaks=<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/seq.html" rel="nofollow">seq</a>(1992, 2005, 1)) +
 geom_segment(aes(xend=<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/max.html" rel="nofollow">max</a>(x)+.20, yend=y), linetype="dotted", size=.1, color=cols) +
 theme(panel.grid.major = element_line(color="black", size=.2),
 panel.grid.minor = element_line(color="grey", size=.2),
 panel.grid.major.y = element_blank(),
 panel.grid.minor.y = element_blank())</pre> </td> 
 </tr> 
 </tbody> 
</table>

![Screenshot_202015-03-10_2018.16.14.png][]

#### Related Posts ####

* January 19, 2015 -- [ ggtree in Bioconductor 3.1][ggtree in Bioconductor 3.1] (15)
 * February 10, 2015 -- [ \[ggtree\] updating a tree view using %<% operator][_ggtree_ updating a tree view using _ operator] (0)
 * December 21, 2014 -- [ viewing and annotating phylogenetic tree with ggtree][viewing and annotating phylogenetic tree with ggtree] (5)
 * April 30, 2014 -- [ visualization methods in ChIPseeker][visualization methods in ChIPseeker] (8)
 * March 27, 2011 -- [ clusterProfiler in Bioconductor 2.8][clusterProfiler in Bioconductor 2.8] (1)

[YGC _ R]: http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/
[R-bloggers]: http://www.r-bloggers.com/
[FigTree]: http://beast.bio.ed.ac.uk/figtree
[Screenshot_202015-03-10_2018.15.57.png]: https://raw.githubusercontent.com/GuangchuangYu/ygc_name/master/2015/Screenshot%202015-03-10%2018.15.57.png
[ggtree]: https://github.com/GuangchuangYu/ggtree
[Link 1]: http://www.ericbess.com/ericblog/2008/03/03/wp-codebox/#examples
[Screenshot_202015-03-10_2018.16.14.png]: https://raw.githubusercontent.com/GuangchuangYu/ygc_name/master/2015/Screenshot%202015-03-10%2018.16.14.png
[ggtree in Bioconductor 3.1]: http://ygc.name/2015/01/19/ggtree-in-bioconductor-3-1/
[_ggtree_ updating a tree view using _ operator]: http://ygc.name/2015/02/10/ggtree-updating-a-tree-view/
[viewing and annotating phylogenetic tree with ggtree]: http://ygc.name/2014/12/21/ggtree/
[visualization methods in ChIPseeker]: http://ygc.name/2014/04/30/visualization-methods-in-chipseeker/
[clusterProfiler in Bioconductor 2.8]: http://ygc.name/2011/03/27/clusterprofiler-bioconductor/