R: Plot "phylepic" objects

plot.phylepic {phylepic}

R Documentation

Plot "phylepic" objects

Description

The autoplot() and plot() methods for "phylepic" objects assemble various panels into the final plot. To facilitate customisations, the plots from each panel can be overwritten. Some effort is made to ensure that the specified plots will look reasonable when assembled.

Usage

## S3 method for class 'phylepic'
plot(
  x,
  ...,
  plot.tree = plot_tree(),
  plot.bars = plot_bars(),
  plot.calendar = plot_calendar(),
  plot.epicurve = plot_epicurve(),
  scale.date = NULL,
  scale.fill = NULL,
  width.tree = 10,
  width.bars = 1,
  width.date = 5,
  width.legend = 2,
  height.tree = 2
)

## S3 method for class 'phylepic'
autoplot(
  object,
  ...,
  plot.tree = plot_tree(),
  plot.bars = plot_bars(),
  plot.calendar = plot_calendar(),
  plot.epicurve = plot_epicurve(),
  scale.date = NULL,
  scale.fill = NULL,
  width.tree = 10,
  width.bars = 1,
  width.date = 5,
  width.legend = 2,
  height.tree = 2
)

Arguments

`...`	Ignored.
`plot.tree`	ggplot for the tree panel (see plot_tree).
`plot.bars`	ggplot for the metadata bars panel (see plot_bars).
`plot.calendar`	ggplot for the calendar panel (see plot_calendar).
`plot.epicurve`	ggplot for the epidemic curve panel (see plot_epicurve).
`scale.date`	A date scale passed to both the calendar and epicurve panels (see ggplot2::scale_x_date).
`scale.fill`	A fill scale passed to both the calendar and epicurve panels (see ggplot2::scale_x_date).
`width.tree`	Relative width of the tree panel.
`width.bars`	Relative width of the metadata bars panel.
`width.date`	Relative width of the calendar panel.
`width.legend`	Relative width of the legend, if present.
`height.tree`	Relative height of the tree panel.
`object`, `x`	Object of class "phylepic".

Details

In general, if you wish to suppress a panel from the plot, set the corresponding ⁠plot.*⁠ argument to NULL. To customise it, use the corresponding ⁠plot_*()⁠ function, which returns a ggplot plot. You can then add new layers or themes to that plot. See vignette("phylepic") for examples.

Legends from all panels are collected and de-duplicated. They are drawn on the right edge of the overall plot.

Value