flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades.
require(ggtree)
set.seed(2015-07-01)
tr <- rtree(30)
p <- ggtree(tr) + geom_text(aes(label=node))
gridExtra::grid.arrange(p, flip(p, 38, 33), ncol=2)
showtext is a neat solution to use various types of fonts in R graphs and make it easy to use funny fonts. With showtext, we can draw phylogenetic tree with different types of fonts even with symbolic/icon fonts.
require(showtext)
font.add.google("Gochi Hand", "gochi")
font.add.google("Rock Salt", "rock")
link = "http://img.dafont.com/dl/?f=wm_people_1";
download.file(link, "wmpeople1.zip", mode = "wb");
unzip("wmpeople1.zip");
font.add("wmpeople1", "wmpeople1.TTF");
link = "http://img.dafont.com/dl/?f=emoticons";
download.file(link, "emoticons.zip", mode = "wb");
unzip("emoticons.zip");
font.add("emoticons", "emoticons.ttf");
showtext.auto()
set.seed(2015-05-14)
library(ggplot2)
library(ggtree)
tree <- rtree(30)
ggtree(tree, color="darkgreen") + geom_tiplab(family="gochi") + theme_classic() +
theme(axis.text.x=element_text(size=rel(4), family="emoticons", color="firebrick")) +
scale_y_continuous(breaks=seq(0, 30, 4), labels=letters[c(12:17, 20, 21)]) +
theme(axis.text.y=element_text(size=rel(4), family="wmpeople1", color="#FDAC4F")) +
annotate("text", x=2, y=18, label="Have fun with ggtree!",
family="rock", angle=30, size=12, color="steelblue")
GOSemSim was first implemented in 2008 and published in Bioinformatics in 2010. It’s now a mature package with no bugs found in the past half year. Only vignette and Information content data were updated.
FigTree is designed for viewing
beast output as demonstrated by their example data:
I am very exciting that I have received very positive feedback from Ahmed Moustafa and Simon Frost.
ggtree now has equipped with
a lot of new features. This time, I would like to introduce the replace
operator, %<%. Suppose we have build a tree view using ggtree with
multiple layers, we don’t need to run the code again to build a new tree
view with another tree. In
ggtree, we provides an operator, %<%, for updating tree view.
When I need to annotate nucleotide substitutions in the phylogenetic tree, I found that all the software are designed to display the tree but not annotating it. Some of them may support annotating the tree with specific data such as bootstrap values, but they are restricted to a few supported data types. It is hard/impossible to inject user specific data.
