ggtree-plotly.Rmd

## Convert a `ggtree` object to a `plotly` object {#plotly}

One way to make a quick interactive phylogenetic tree is using `r Biocpkg("ggtree")` with the `r CRANpkg("plotly")` package. The [ggplotly()](https://plotly-r.com/improving-ggplotly.html) is able to convert `ggtree` object to a `plotly` object. Note that the `r Biocpkg("ggtree")` package also supports interactive manipulation of the phylogenetic tree via the [identify()](#identify) method.


```r
# example from https://twitter.com/drandersgs/status/965996335882059776

# 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)
```


(ref:ggtreeplotlyscap) Interactive phylogenetic tree by combining ggtree with plotly.

(ref:ggtreeplotlycap) **Interactive phylogenetic tree by combining ggtree with plotly.**



```{r ggtreeplotly, fig.cap="(ref:ggtreeplotlycap)", fig.scap="(ref:ggtreeplotlyscap)", echo=FALSE, out.width='100%'} 
knitr::include_graphics("img/ggtree-plotly.gif")
```