ggtree for visualization and annotation of phylogenetic trees
YU Guangchuang (余光创)
YU Guangchuang
Models are approximations or simplications of real-world systems
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(((virus2:0.39,virus1):0.28):0.2,
virus3):0.26):0.54,
(virus5:0.53,virus4))):0.1):0.41):0.92):0.98,
virus7)):0.02):0.08):0.83,
((virus10:0.85,virus9)):0.5):0.98);
R is still limited
df <- fortify(merged_tree)
df <- df[, c("dN_vs_dS", "dN", "dS", "rate")]
df <- na.omit(df)
df <- df[df$dN_vs_dS >=0 & df$dN_vs_dS <=1.5,] %>%
tidyr::gather(type, value, dN_vs_dS:dS)
df$type[df$type == "dN_vs_dS"] <- "dN/dS"
df$type %<>% factor(., levels=c("dN/dS", "dN", "dS"))
ggplot(df, aes(rate, value)) + geom_hex() +
facet_wrap(~type, scale="free_y")
ggtree packageggplot2 to support tree objects
geom_tree: geometric layer to support tree structurep <- ggplot(beast_tree, aes(x,y)) + geom_tree() 
theme_tree & theme_tree2multiplot(p + theme_tree(), p + theme_tree2(), ncol=2)
ggtree = ggplot() + geom_tree() + theme_tree()ggtree(beast_tree)
ggtree = ggplot() + geom_tree() + theme_tree()ggtree(beast_tree, branch.length='none', color='slateblue',
layout='fan', open.angle=180, size=2)
ggtree = ggplot() + geom_tree() + theme_tree()ggtree(beast_tree, aes(color=rate), linetype='dashed')
ggplot2 can be used directly in ggtreep <- ggtree(beast_tree)
(p + geom_point(aes(color=isTip), size=1) +
geom_text(aes(label=round(posterior*100)),
hjust=-.1, size=2.5)) %>% viewClade(node=118) 
(p + geom_point2(aes(subset= !is.na(posterior) & posterior > .75),
color='firebrick')) %>% viewClade(node=118)
geom_treescale displays the tree scalep <- p + geom_treescale(x=0, y=10, offset=2)
geom_tiplab: layer of tip labels (taxa names)p2 <- p + geom_tiplab(size=2)
p <- p + geom_tiplab(align=T, size=2, linesize=.3) + xlim(NA, 30)
multiplot(p2, p, ncol=2)
geom_hilight: highlight clade with background colorp <- p + geom_hilight(node=118, fill='blue', alpha=.4)
geom_cladelabel: labeling cladep <- p + geom_cladelabel(118, 'a selected clade', offset=6.5, offset.text=.5,
barsiz=3, color='darkgreen', angle=90, hjust='center')
geom_range: displays uncertainty of branch lengthsp <- p + geom_range('height_0.95_HPD', color='red', alpha=.5)
geom_taxalink: connecting related taxap <- p + geom_taxalink(45, 19, color='purple', arrow=arrow(length=unit(0.02, 'npc'))) +
geom_taxalink(46, 18, color='blue', arrow=arrow(length=unit(0.02, 'npc')))
## p + geom_tippoint(aes(color=grepl("Swine", label)))
tip <- get.tree(beast_tree)$tip.label
host <- rep("Human", length(tip))
host[grep("Swine", tip)] <- "Swine"
host.df <- data.frame(taxa=tip, host=host)
p %<+% host.df + geom_tippoint(aes(color=host))
library(ggtree)
beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")
beast_tree <- read.beast(beast_file)
ggtree(beast_tree) + geom_treescale(x=0, y=10, offset=2) +
geom_tiplab(align=T, size=2, linesize=.3) + xlim(NA, 30) +
geom_hilight(node=118, fill='blue', alpha=.4) +
geom_cladelabel(118, 'a selected clade', offset=6.5,
offset.text=.5, barsiz=3, color='darkgreen',
angle=90, hjust='center') +
geom_range('height_0.95_HPD', color='red', alpha=.5) +
geom_taxalink(45, 19, color='purple',
arrow=arrow(length=unit(0.02, 'npc'))) +
geom_taxalink(46, 18, color='blue',
arrow=arrow(length=unit(0.02, 'npc'))) +
geom_tippoint(aes(color=grepl("Swine", label)))
p1 <- ggtree(merged_tree, aes(color=rate)) +
theme_tree2() + geom_tiplab(size=1.5) +
scale_color_continuous(high='red', low='green')
p2 <- p1 %<% rescale_tree(merged_tree, 'dN') + aes(color=dN)
multiplot(p1+xlim(NA, 25)+ggtitle('time-scaled tree'),
p2+xlim(NA, 0.07)+ggtitle('dN tree'), ncol=2)
ggplot2
