reproduce OutbreakTools example using ggtree

OutbreakTools example

This example is presented in vignette of OutbreakTools.

library(OutbreakTools)
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)

x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna,
      dna.individualID = samples$individualID, dna.date = samples$date,
      trees = FluH1N1pdm2009$trees)

p <- plotggphy(x, ladderize = TRUE, branch.unit = "year",
               tip.color = "location", tip.size = 3, tip.alpha = 0.75)

In this figure, it use Date as x-axis and annotate the tree with Location. In epidemic time and location that isolate the virus is important information and plotggphy is designed for viewing such information.

reproduce using ggtree

In ggtree, it's very easy to reproduce such figure by adding a layer of location information.

library(ggtree)
tree <- x@trees[[1]]
g <- ggtree(tree, right=T, mrsd="2009-09-30") + theme_tree2()
g <- g + theme(panel.grid.major = element_line(color="grey"), 
               panel.grid.major.y=element_blank())

## extract location info
meta.df <- x@dna@meta
meta.df <- data.frame(taxa=rownames(meta.df), meta.df)
loc <- x@individuals
loc <- data.frame(individualID=rownames(loc), loc)
meta_loc <- merge(meta.df, loc, by="individualID")
meta_loc <- meta_loc[,-1]

## attach additional information to tree view via %<+% operator 
## that was created in ggtree
g <- g %<+% meta_loc

g + geom_tippoint(aes(color=location), size=3, alpha=.75) + 
    theme(legend.position="right") + 
      scale_color_brewer("location", palette="Spectral")

benchmark

require(microbenchmark)

draw_ggtree <- function(x) {
	tree <- x@trees[[1]]
	g <- ggtree(tree, right=T, mrsd="2009-09-30") + theme_tree2()
	g <- g + theme(panel.grid.major = element_line(color="grey"), 
	               panel.grid.major.y=element_blank())

	## extract location info
	meta.df <- x@dna@meta
	meta.df <- data.frame(taxa=rownames(meta.df), meta.df)
	loc <- x@individuals
	loc <- data.frame(individualID=rownames(loc), loc)
	meta_loc <- merge(meta.df, loc, by="individualID")
	meta_loc <- meta_loc[,-1]

	## attach additional information to tree view via %<+% operator 
	## that was created in ggtree
	g <- g %<+% meta_loc

	g + geom_tippoint(aes(color=location), size=3, alpha=.75) + 
	    theme(legend.position="right") + 
	      scale_color_brewer("location", palette="Spectral")
}

bm <- microbenchmark(
	OutbreakTools = plotggphy(x, ladderize = TRUE, branch.unit = "year",
                   tip.color = "location", tip.size = 3, tip.alpha = 0.75),
   	ggtree = draw_ggtree(x),
	times=100L
)

print(bm)
## Unit: milliseconds
##           expr      min       lq      mean   median        uq       max neval
##  OutbreakTools 564.0195 585.7710 1225.8299 1767.713 1784.8457 1984.3352   100
##         ggtree 144.2246 151.7099  159.3318  155.200  160.9121  328.2016   100

qplot(y=time, data=bm, color=expr)  + ggtitle("run time comparison")