Plot for class simul_process — plot.params

This function takes an object of class params_process, and plots them along with some data at the tips of the tree.

# S3 method for params_process
plot(
  x,
  phylo,
  data = NULL,
  traits,
  automatic_colors = TRUE,
  color_characters = "black",
  color_edges = "black",
  plot_ancestral_states = FALSE,
  ancestral_states = NULL,
  imposed_scale,
  ancestral_cex = 2,
  ancestral_pch = 19,
  value_in_box = FALSE,
  ancestral_as_shift = FALSE,
  shifts_cex = 0.6,
  shifts_bg = "chocolate4",
  root_bg = "chocolate4",
  shifts_adj = 0,
  root_adj = 1,
  color_shifts_regimes = FALSE,
  regime_boxes = FALSE,
  alpha_border = 70,
  show.tip.label = FALSE,
  label_cex = 0.5,
  label_offset = 0,
  axis_cex = 0.7,
  edge.width = 1,
  margin_plot = NULL,
  gray_scale = FALSE,
  ...
)

Arguments

x: an object of class params_process.
phylo: a phylogenetic tree.
data: a matrix of data at the tips of the tree. Must have p rows and ntaxa columns. If these are simulated, use the extract.simul_process function.
traits: a vector of integers giving the numbers of the trait to be plotted. Default to 1:p (all the traits).
automatic_colors: whether to color the edges automatically according to their regimes. Default to TRUE. If FALSE, colors can be manually specified through arguments color_characters and colro_edges (see below).
color_characters: if automatic_colors=FALSE, a vector of colors for the tips of the tree.
color_edges: if automatic_colors=FALSE, a vector of colors for the edges of the tree.
plot_ancestral_states: whether to plot the ancestral traits inferred at the internal nodes of the tree. Only available if only one trait is plotted. Default to FALSE.
ancestral_states: if plot_ancestral_states=TRUE, the ancestral states must be specified. If these are simulated, use the extract.simul_process function.
imposed_scale: if plot_ancestral_states=TRUE, a vector specifying the imposed scale for the ancestral states plotting. Useful to make comparisons. Default to the plotted trait.
ancestral_cex: if plot_ancestral_states=TRUE, the size of the ancestral states on the tree. Default to 2.
ancestral_pch: if plot_ancestral_states=TRUE, the symbol used of the ancestral states. Default to circles (pch=19).
value_in_box: whether to plot the value of the shift in a box on the edges. Only available when only one trait is plotted. Can be difficult to read on big trees. The size of the text in the boxes is controlled by parameter. Default to FALSE.
ancestral_as_shift: whether to represent the ancestral value at the root as an ancestral shift on the root edge. Default to FALSE. shifts_cex (see below).
shifts_cex: if value_in_box=TRUE, the size of the text in the boxes. Default to 0.8.
shifts_bg: if value_in_box=TRUE, the background color of the boxes.
root_bg: if value_in_box=TRUE and ancestral_as_shift=TRUE, the background color of the ancestral box.
shifts_adj: the adj parameter for the shifts position on the edges. Default to 0 (beginning of the edge).
root_adj: if ancestral_as_shift=TRUE, the adj parameter for the ancestral value position on the root edge. Default to 1.
color_shifts_regimes: whether to color each shift according to its regime (default to the same color of the edge it's on). Default to FALSE.
regime_boxes: whether to draw a box showing all the tips below a given. The transparency of the border of the box is controlled by parameter alpha_border (see below).
alpha_border: if regime_boxes=TRUE, the alpha parameter of the border of the box. Default to 70.
show.tip.label: whether to show the tip labels. Default to FALSE.
label_cex: if show.tip.label=TRUE, the size of the labels. Default to 0.5.
label_offset: if show.tip.label=TRUE, the size of the offset between the tree and the labels. Default to 0.
axis_cex: cex for the label values of the plot. Default to 0.7.
edge.width: width of the edge. Default to 1.
margin_plot: vector giving the margin to around the plot. Default to c(0, 0, 0, 0).
gray_scale: if TRUE, the colors are replaced by a gray scale. Default to FALSE.
...: further arguments to be passed to plot.phylo.

Plot for class `simul_process`

Arguments

See also