phylepic

Phylepic contains tools for visualisations that are useful for genomic epidemiology of pathogens, designed for a public health setting.

Installation

You can install phylepic like so:

# CRAN release
install.packages('phylepic')

# development version
install.packages('phylepic', repos = c('https://cidmp-ph.r-universe.dev', 'https://cloud.r-project.org'))

Example

This is an example of a very minimal phylepic chart.

library(ape)
library(phylepic)

tree <- read.tree(text = "((D:0.3,C:0.4):0.5,B:0.1,A:0.2);")
metadata <- data.frame(
  ID = c("A", "B", "C", "D"),
  date = as.Date(c("2024-01-10", "2024-01-12", "2024-01-21", "2024-01-23")),
  country = factor(c("Australia", "Australia", NA, "New Zealand"))
)

phylepic(tree, metadata, ID, date) |> plot()

Refer to the package vignette for a more complete example.

Citation

See citation("phylepic").

Suster CJE, Watt AE, Wang Q, Chen SC, Kok J, Sintchenko V (2024). “Combined visualization of genomic and epidemiological data for outbreaks.” Epidemiology & Infection 152: e110. doi:10.1017/S0950268824001092,