Created
February 20, 2018 03:54
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Quick interactive phylogenetic tree in R
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# 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) |
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?
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re @gotwals it seems as though the same general output can be achieved by switching to geom_text i.e.: