Visualizing trees of many genes quickly with ggtree can be executed using the following steps:

1. Load the libraries and get a phylo object of the Newick tree:

library(ggplot2)
library(ggtree)
itol <-ape::read.tree(file.path(getwd(), "datasets", "ch4", "itol.nwk")) 

2.  Make a basic tree plot:

ggtree(itol)

3. Make a circular plot:

ggtree(itol, layout = "circular")

4. Rotate and invert the tree:

ggtree(itol) + coord_flip() + scale_x_reverse()

5. Add labels to the tree tips:

ggtree(itol) + geom_tiplab( color = "blue", size = 2)

6. Make a strip of color to annotate a particular clade:

ggtree(itol, layout = "circular") + geom_strip(13,14, color="red", barsize = 1)

7. Make a blob of color to highlight a particular clade:

ggtree(itol, layout = "unrooted") + geom_hilight_encircle(node = 11, fill = "steelblue")