Combined Visualisation of Phylogenetic and Epidemiological Data
Out of bounds handling
Cartesian coordinates with specialised grid for trees
Create a graph layout for plotting
Drop a clade from a phylogentic tree
Specialised tile geometry for calendar plots
Annotate nodes with text and a background
Plot epidemic curve panel
phylepic: Combined Visualisation of Phylogenetic and Epidemiological D...
Combine metadata (a line list) with a phylogenetic tree
Plot "phylepic" objects
Plot metadata bars panel
Plot calendar panel
Plot phylogenetic tree panel
Date scale with breaks specified by week
Calculate week bins from dates
Calculate week bins with additional binning in the y axis
Breaks for week-binning date axes
A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
Useful links