Package index • 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

Calendar drawing

geom_calendar(): Specialised rectangular geometry for calendar plots

stat_bin_location(): Annotate rows with 2D bin positions

oob_infinite(): Out of bounds handling

Week binning

scale_x_week(): Date scale with breaks specified by week

week_breaks(): Breaks for week-binning date axes

Automatic binning

stat_bin_auto(): Calculate bins using scale breaks

stat_bin_2d_auto(): Calculate two-dimensional bins using scale breaks

breaks_cached(): Cached scale break function

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