A question on biostars asking how to generate the following figure:
This can be quite easy to implement in ggtree, I can write a
geom layer to layout the alignment. As ggbio already provides many
geom for genomic data and I don’t want to re-invent the wheel, I decided to try
ggtree+ggbio. This is also the beauty of
R that packages complete each others.
OutbreakTools implements basic tools for the analysis of Disease Outbreaks.
obkData to store case-base outbreak data. It also provides a function,
plotggphy, to visualize such data on the phylogenetic tree.
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) plotggphy(x, ladderize = TRUE, branch.unit = "year", tip.color = "location", tip.size = 3, tip.alpha = 0.75)
ggtree can parse many software outputs and the evolution evidences inferred by these software can be used directly for tree annotation. ggtree not only works as an infrastructure that enables evolutionary data that inferred by commonly used software packages to be used in R, but also serves as a general tree visualization and annotation tool for the R community as it supports many S3/S4 objects defined by other R packages.
phyloseq class defined in the phyloseq package was designed for microbiome data.
phyloseq package implemented
plot_tree function using
ggplot2. Although the function was implemented by
ggplot2 and we can use
scale_color_manual etc for customization, the most valuable part of
ggplot2, adding layer, is missing.
plot_tree only provides limited parameters to control the output graph and it is hard to add layer unless user has expertise in both