ggjoy 和ggtree：双剑合璧，惊艳无比

之前介绍了《 joyplot：一种波涛汹涌，哦不对，是山峰叠峦的可视化方式 》，最近有人问怎么和ggtree搞基，像这样的问题，大家应该不陌生，因为我在《 align genomic features with phylogenetic tree 》一文中已经直播了和ggbio的搞基过程。

我在《 how to bug author 》一文中，就强调了在社区里问问题的重要性，想要ggjoy和ggtree搞基的问题，就没有直接问我，而是在同性交友网站stackoverflow上问，在我回答之前，就已经有非常好的解答贴出来了，这就是社区的好处！公开交流比私下邮件好多了。

问题

Is it possible to add a joyplot as a panel to a plot that includes a ggtree, as shown in these examples? Examples of joyplots are here.

• https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/

• https://katherinemwood.github.io/post/joy/

I realize that I could manually put the species labels for the joyplot in the same order as the tree tip labels, but I am looking for an automatic solution. I would like to associate the joyplot rows with the tips of the trees automatically, akin to how the boxplot data are associated with the tip labels.

I think that Guangchuang Yu’s examples at the above link provide suitable data:

require(ggtree)
require(ggstance)# generate tree

tr 30)# create simple ggtree object with tip labels
p 0.02)
# Generate categorical data for each "species"
d1 "GZ", "HK", "CZ"), 30, replace=TRUE))
#Plot the categorical data as colored points on the tree tips

p1 # Generate distribution of points for each species

d4 = data.frame(id=rep(tr$tip.label, each=20), 
            val=as.vector(sapply(1:30, function(i) 
                            rnorm(20, mean=i)))
            )               

# Create panel with boxplot of the d4 data
p4 "Boxplot", data=d4, geom_boxploth, 
        mapping = aes(x=val, group=label, color=location))           
plot(p4)

This produces the plot below:

Is it possible to create a joyplot in place of the boxplot?

Here is code for a quick joyplot of the demo dataset d4 above:

require(ggjoy)

ggplot(d4, aes(x = val, y = id)) + 
geom_joy(scale = 2