wrapping labels in ggplot2

February 14, 2017 in R

在公众号biobabble后台有多人同时在问这个问题：

晒这个截屏主要想说一点，如果是一两句话就能说清楚的问题，可以提问，如果不是，则不要在后台提问，写邮件或者到论坛提问，是更好的方式，像截屏中显示的，图片显示过期，我根本就没看到过图片。在手机上是无法看的，而我正好几天没在电脑前，于是你们发的图片我看不了，而且我如果没有在24小时之内回复，公众平台就不允许我回复了，因为问题已经过期。所以在此强调，不要在后台发图片提问，不要在后台问稍复杂的问题。

这个问题其实很简单，用stringr包的str_wrap来完成文本自动换行就行了。

add layer to specific panel of facet_plot output

December 28, 2016 in R, Visualization, Evolution

This is a question from ggtree google group:

Dear ggtree team,

how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, so I don’t know which subsetting to use. I have already read http://stackoverflow.com/questions/29873155/geom-text-and-facets-not-working
  tr <- rtree(30)
  
  d1 <- data.frame(id=tr$tip.label, val=rnorm(30, sd=3))
  p <- ggtree(tr)
  
  p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='firebrick')
  d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))
  
  p3 <- facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()
Thanks! Andreas

If this can be done, we can create even more comprehensive tree plots.

xlim_tree: set x axis limits for only Tree panel

October 31, 2016 in R, Visualization, Evolution

A ggtree user recently asked me the following question in google group:

I try to plot long tip labels in ggtree and usually adjust them using xlim(), however when creating a facet_plot xlim affects all plots and minimizes them.

Is it possible to work around this and only affect the tree and it’s tip labels leaving the other plots in facet_plot unaffected?

This is indeed a desire feature, as ggplot2 can’t automatically adjust xlim for text since the units are in two different spaces (data and pixel).

facet_plot: a general solution to associate data with phylogenetic tree

October 26, 2016 in R, Visualization, Evolution

ggtree provides gheatmap for visualizing heatmap and msaplot for visualizing multiple sequence alignment with phylogenetic tree.

We may have different data types and want to visualize and align them with the tree. For example, dotplot of SNP site (e.g. using geom_point(shape='|')), barplot of trait values (e.g. using geom_barh(stat='identity')) et al.

To make it easy to associate different types of data with phylogenetic tree, I implemented the facet_plot function which accepts a geom function to draw the input data.frame and display it in an additional panel.

reproducible logo generated by ggtree

October 14, 2016 in R, Visualization

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.

Here, as examples, I used ggtree to draw capital character G and C, which are first letter of my name :-).

To draw a tree in such shape, we need fan layout (circular layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the G and C shapes of tree. I am thinking about using the G shaped tree as ggtree logo. Have fun with ggtree :-)

embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function

March 20, 2016 in R, Visualization

I extended the subview function to support embed image file in a ggplot object.

set.seed(123)
d = data.frame(x=rnorm(10), y=rnorm(10))

imgfile <- tempfile(, fileext=".png")
download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140",
	          destfile=imgfile, mode='wb')

p = ggplot(d, aes(x, y))
subview(p, imgfile, x=d$x[1], y=d$y[1]) + geom_point(size=5)