vignettePlot: Vignette Plot

In TGuillerme/Inapp: Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees

Vignette Plot

Description

Creates a plot formatted for inclusion in vignettes

Usage

vignettePlot(
  tree,
  character,
  na = TRUE,
  legend.pos = "bottomleft",
  passes = if (na) 1:4 else 1:2,
  state.labels = character(0),
  counts = if (na) 1:2 else 2,
  state.override = NULL,
  score.override = NULL,
  changes.override = NULL,
  regions.override = NULL,
  ...
)

Arguments

tree	Tree to plot
character	character string listing character states to plot; tokens will be matched to labels in alphabetical order.
na	logical, should - be treated as inapplicable?
legend.pos	character Position to plot legend.
passes	integer specifying which passes to plot; specify 0 for none.
state.labels	Will be passed directly to plot.states.matrix
counts	integer vector specifying which counts to show: see plot.states.matrix for details
state.override	list specifying states to reconstruct at each tip and node, instead of those reconstructed
score.override, changes.override, regions.override	integers to override the values calculated
...	Additional parameters to pass to plot.states.matrix.

Author(s)

Martin R. Smith

TGuillerme/Inapp documentation built on Feb. 4, 2024, 7:26 a.m.