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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:

# 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 [Preprint].” medRxiv. doi:10.1101/2024.04.02.24305229,

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.