News of ggtree

December 30, 2015 in R

A new version of ggtree that works with ggplot2 (version >= 2.0.0) is now availabel.

new layers

Some functions, add_legend, hilight, annotation_clade and annotation_clade2 were removed. Instead we provide layer functions, geom_treescale, geom_hilight and geom_cladelabel. You can use + operator to add layers using these layer functions.

In addtion, we provide geom_point2, geom_text2 and geom_segment2 which works exactly as geom_point, geom_text and geom_segment except they allow ggtree users to do subsetting.

use emoji font in R

December 16, 2015 in R, Visualization

![](http://guangchuangyu.github.io/blog_images/2015/Screenshot 2015-12-16 10.55.49.png)

I have played with emoji in R for a while. My solution of using it is different from what implemented in emoGG.

emoGG is a good attemp to add emoji in ggplot2. It render emoji picture (png) and creat a layer, geom_emoji, to add emoji.

In my opinion, emoji should be treated as ordinary font in user interface, albeit it maynot be true internally.

It would be more flexible if we can use emoji as ordinary font and in this way user don’t need to learn extra stuff.

[Bioc 32] NEWS of my BioC packages

October 15, 2015 in R

In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes.

GOSemSim

To make it consistent between GOSemSim and clusterProfiler, ‘worm’ was deprecated and instead we should use ‘celegans’. As usual, information content data was updated.

subsetting data in ggtree

September 24, 2015 in R

Subsetting is commonly used in ggtree as we would like to for example separating internal nodes from tips. We may also want to display annotation to specific node(s)/tip(s).

Some software may stored clade information (e.g. bootstrap value) as internal node labels. Indeed we want to manipulate such information and taxa labels separately.

In current ggplot2 (version=1.0.1, access date:2015-09-23), it support subset. For instance:

comic phylogenetic tree with ggtree and comicR

September 8, 2015 in R

ggtree applies the concepts of grammar of graphic in phylogenetic tree presentation and make it easy to add multiple layers of text and even figures above a 🌲.

Here, I cartoonize a phylogenetic tree generated by ggtree with comicR, which is a funny package to generate comic (xkcd-like) graph in R. Have fun with ggtree and comicR.

subview

August 31, 2015 in Visualization, R

I implemented a function, subview, in ggtree that make it easy to embed a subplot in ggplot.

An example is shown below:

library(ggplot2)
library(ggtree)

dd <- data.frame(x=LETTERS[1:3], y=1:3)
pie <- ggplot(dd, aes(x=1, y, fill=x)) + 
	geom_bar(stat="identity", width=1) + 
	coord_polar(theta="y") + theme_tree() + 
	xlab(NULL) + ylab(NULL) + 
	theme_transparent()

x <- sample(2:9)
y <- sample(2:9)
width <- sample(seq(0.05, 0.15, length.out=length(x)))
height <- width

p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()
print(p)
for (i in seq_along(x)) {
	p %<>% subview(pie, x[i], y[i], width[i], height[i])
	print(p)
}