Quick interactive phylogenetic tree in R

interative_tree.R

# LOAD LIBS ---------------------------------------------------------------
library(ape)
library(ggtree)
library(plotly)

# CREATE A TREE -------------------------------------------------------------
n_samples <- 20
n_grp <- 4
tree <- ape::rtree(n = n_samples)

# CREATE SOME METADATA ----------------------------------------------------
id <- tree$tip.label
set.seed(42)
grp <- sample(LETTERS[1:n_grp], size = n_samples, replace = T)
dat <- tibble::tibble(id = id,
                      grp = grp)

# PLOT THE TREE -----------------------------------------------------------
p1 <- ggtree(tree)

metat <- p1$data %>%
  dplyr::inner_join(dat, c('label' = 'id'))

p2 <- p1 +
  geom_point(data = metat,
             aes(x = x,
                 y = y,
                 colour = grp,
                 label = id))

plotly::ggplotly(p2)

Note that I am cheating a bit. I added label to the aes in geom_point to get that info when mousing over. For that, I get a warning when I run the code above about ignoring the unknown aesthetic label.

Thanks, good stuff. How can you remove the duplicate x and y labels?

@teshu02 You can specify which aesthetics show when mousing over nodes by setting the tooltip parameter within the ggplotly function.

Example using above snippet:
plotly::ggplotly(p2, tooltip = "label")

I can not get the other layout options of ggtree to work properly. I get warnings and just part of the plot. Do you know how can I fix this?

I get an error with the aesthetic label: Warning: Ignoring unknown aesthetics: label

re @gotwals it seems as though the same general output can be achieved by switching to geom_text i.e.:

p2 <- p1 +
  geom_text(data = metat,
             aes(x = x,
                 y = y,
                 colour = grp,
                 label = id))

I don't know if you can see this, but this code works really well.
Is there any way to additionally display the bootstrap value or tip label as the ID of the sample rather than the group?