Function reference • phylepic

Phylepic charts

phylepic(): Combine metadata (a line list) with a phylogenetic tree

plot(<phylepic>) autoplot(<phylepic>): Plot "phylepic" objects

plot_bars(): Plot metadata bars panel

plot_calendar(): Plot calendar panel

plot_epicurve(): Plot epidemic curve panel

plot_tree(): Plot phylogenetic tree panel

Week-binned dates

geom_calendar(): Specialised tile geometry for calendar plots

scale_x_week(): Date scale with breaks specified by week

stat_week(): Calculate week bins from dates

stat_week_2d(): Calculate week bins with additional binning in the y axis

week_breaks(): Breaks for week-binning date axes

oob_infinite(): Out of bounds handling

Phylogenetic tree drawing

coord_tree(): Cartesian coordinates with specialised grid for trees

create_tree_layout(): Create a graph layout for plotting

geom_node_text_filled(): Annotate nodes with text and a background

drop.clade(): Drop a clade from a phylogentic tree