将ggdend树与geom_scatterpie组合

Question

I have a phylogenetic tree:

my.tree <- ape::read.tree(text = "((rat:0.06290316531,mouse:0.06094803666):0.05175420892,human:0.09883650566);")

which I then convert to a ggdend object:

library(dplyr)
my.dend <- phylogram::as.dendrogram.phylo(my.tree) %>%
  dendextend::hang.dendrogram() %>%
  dendextend::hang.dendrogram(hang = -1) %>%
  dendextend::as.ggdend()

I would like to plot my.dend using ggplot2 and to add to the leaves pie charts.

Here is the data.frame that describes the pie for each leaf:

set.seed(1)
labels.df <- data.frame(label = c("human","mouse","rat"),t(apply(matrix(runif(9,0,1),3,3),1,function(x) x/sum(x))),check.names = F) %>%
  dplyr::left_join(my.dend$labels %>% dplyr::select(x,y,label))

I thought that combining the plotting of my.dend with labels.df using scatterpie 's geom_scatterpie can work.

So I do:

library(ggplot2)
library(scatterpie)

ggplot(my.dend,labels=F,horiz=T)+guides(fill=F)+coord_flip()+annotate("text",size=4.5,hjust=0,x=my.dend$label$x,y=my.dend$label$y,label=my.dend$label$label)+labs(x="",y="")+theme_minimal()+
  theme(axis.text=element_blank(),axis.ticks=element_blank(),panel.grid=element_blank(),legend.position="none",legend.text=element_blank(),legend.background=element_blank(),legend.key=element_blank())+
  geom_scatterpie(aes(x=x,y=y+0.05),data=labels.df,color=NA,cols=as.character(1:3))

Which gives:

If add +coord_flip() to the end:

ggplot(my.dend,labels=F,horiz=T)+guides(fill=F)+coord_flip()+annotate("text",size=4.5,hjust=0,x=my.dend$label$x,y=my.dend$label$y,label=my.dend$label$label)+labs(x="",y="")+theme_minimal()+
  theme(axis.text=element_blank(),axis.ticks=element_blank(),panel.grid=element_blank(),legend.position="none",legend.text=element_blank(),legend.background=element_blank(),legend.key=element_blank())+
  geom_scatterpie(aes(x=x,y=y+0.05),data=labels.df,color=NA,cols=as.character(1:3))+coord_equal()

The pies do not get distorted but the tree flips to become vertical - root facing down:

Any idea how to get the pies not distorted and the tree horizontal with the root on the left?

Answer 1

Looks like it'll be easier to plot the phylogeny and scatterpie separately and then combine them:

Data:

my.tree <- ape::read.tree(text = "((rat:0.06290316531,mouse:0.06094803666):0.05175420892,human:0.09883650566);")

library(dplyr)
my.dend <- phylogram::as.dendrogram.phylo(my.tree) %>%
  dendextend::hang.dendrogram() %>%
  dendextend::hang.dendrogram(hang = -1) %>%
  dendextend::as.ggdend()

set.seed(1)
labels.df <- data.frame(label = c("human","mouse","rat"),t(apply(matrix(runif(9,0,1),3,3),1,function(x) x/sum(x))),check.names = F) %>%
  dplyr::left_join(my.dend$labels %>% dplyr::select(x,y,label))

library(ggplot2)
library(scatterpie)

Plots:

my.dend <- ggplot(my.dend,labels=F,horiz=T)+guides(fill=F)+coord_flip()+annotate("text",size=4.5,hjust=0,x=my.dend$label$x,y=my.dend$label$y,label=my.dend$label$label)+labs(x="",y="")+theme_minimal()+theme_void()
my.scatterpie <- ggplot()+geom_scatterpie(aes(x=y,y=x,r=0.1),data=labels.df,color=NA,cols=as.character(1:3))+coord_equal()+labs(x="",y="",fill="Cluster")+theme_minimal()+theme_void()

gridExtra::grid.arrange(grobs=list(my.dend,my.scatterpie),ncol=2,nrow=1)

And we get:

Would be nice to be able to shrink some of the space that separates the tree from the pies, if anyone can add that.