I would need help in order to add information within a plot.

Here is the plot :

(Code to get this plot below)

And I would like to add a new element with families information stored in this tab:

   labels     family
1      t2  Hominidae
2      t4  Hominidae
3      t3  Hominidae
4     t10    Equidae
5      t5    Equidae
6      t7  Muridae
7      t6    Muridae
8      t1 Crisetidae
9      t8 Crisetidae
10     t9   Outgroup

(dput format)

structure(list(labels = c("t2", "t4", "t3", "t10", "t5", "t7", 
"t6", "t1", "t8", "t9"), family = c("Hominidae", "Hominidae", 
"Hominidae", "Equidae", "Equidae", "Murinidae", "Muridae", "Crisetidae", 
"Crisetidae", "Outgroup")), class = "data.frame", row.names = c(NA, 
-10L))

And get a new figure such as ;

As you can see, I sued the information stored in the tab to add vertical bars followed by the name of the family for each labels.

I found this post related (http://www.randigriffin.com/2017/05/11/primate-phylogeny-ggtree.html) , but it does not do it with geom_bars, it simply add the family annotations next to tree label...

   library(ggplot2)
library(ggtree)

set.seed(2019-10-31)
tr <- rtree(10)

d1 <- data.frame(
  # only some labels match
  label = c(tr$tip.label[sample(9, 9)], "A"),
  value = sample(1:10, 10))

d2 <- data.frame(
  label = rep(tr$tip.label, 5),
  category = rep(LETTERS[1:5], each=10),
  value = rnorm(50, 0, 3)) 

g <- ggtree(tr)   geom_tiplab(align=TRUE)   hexpand(.01)

d2$label <- factor(d2$label, levels = rev(get_taxa_name(g)))
d1$label <- factor(d1$label, levels = rev(get_taxa_name(g)))

p1 <- ggplot(d1, aes(label, value))   geom_col(aes(fill=label))   
  geom_text(aes(label=label, y= value .1))  
  coord_flip()   theme_tree2()   theme(legend.position='none')

p2 <- ggplot(d2, aes(x=category, y=label))   
  geom_tile(aes(fill=value))   scale_fill_viridis_c()   
  theme_minimal()   xlab(NULL)   ylab(NULL)  theme(legend.position='none')


cowplot::plot_grid(g, p2, p1, ncol=3) 

CodePudding user response：

Using a left_join and facets:

d1 <- dplyr::left_join(d1, tab, by = c(label = "labels"))

p1 <- ggplot(d1, aes(label, value))   geom_col(aes(fill=label))   
  geom_text(aes(label=label, y= value .1))  
  coord_flip()   theme_tree2()   theme(legend.position='none')  
  facet_grid(family~., scales = "free_y", space = "free_y")  
  scale_x_discrete(expand = c(0, 0), position = "top")  
  theme(plot.margin = margin(10, 10, 10, 0),
        axis.line.y.right = element_line(size = 3),
        strip.background = element_blank(),
        strip.placement = "outside")

p2 <- ggplot(d2, aes(x=category, y=label))   
  geom_tile(aes(fill=value))   
  scale_fill_viridis_c()   
  theme_minimal()   
  xlab(NULL)   
  ylab(NULL)  
  theme(legend.position='none')


cowplot::plot_grid(g, p2, p1, ncol=3)