Combined Visualisation of Phylogenetic and Epidemiological Data


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Documentation for package ‘phylepic’ version 0.3.0

Help Pages

autoplot.phylepic Plot "phylepic" objects
breaks_cached Cached scale break function
CoordTree Cartesian coordinates with specialised grid for trees
coord_tree Cartesian coordinates with specialised grid for trees
create_tree_layout Create a graph layout for plotting
drop.clade Drop a clade from a phylogentic tree
GeomCalendar Specialised rectangular geometry for calendar plots
GeomTextFilled Annotate nodes with text and a background
geom_calendar Specialised rectangular geometry for calendar plots
geom_node_text_filled Annotate nodes with text and a background
oob_infinite Out of bounds handling
phylepic Combine metadata (a line list) with a phylogenetic tree
plot.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
scale_x_week Date scale with breaks specified by week
StatBin2dAuto Calculate two-dimensional bins using scale breaks
StatBinAuto Calculate bins using scale breaks
StatBinLocation Annotate rows with 2D bin positions
stat_bin2d_auto Calculate two-dimensional bins using scale breaks
stat_bin_2d_auto Calculate two-dimensional bins using scale breaks
stat_bin_auto Calculate bins using scale breaks
stat_bin_location Annotate rows with 2D bin positions
week_breaks Breaks for week-binning date axes