Plot for class PhyloEM

This function takes an object of class PhyloEM, result of function PhyloEM, and plots the result of the inference.

Usage

# S3 method for class 'PhyloEM'
plot(
  x,
  traits = 1:(x$p),
  params = NULL,
  method.selection = NULL,
  automatic_colors = TRUE,
  color_characters = "black",
  color_edges = "black",
  plot_ancestral_states = FALSE,
  name_trait = "Trait Value",
  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_font = 1,
  label_offset = 0,
  axis_cex = 0.7,
  axis_las = 0,
  show_axis_traits = TRUE,
  edge.width = 1,
  margin_plot = NULL,
  gray_scale = FALSE,
  root.edge = TRUE,
  ...
)

Arguments

x

an object of class PhyloEM, result of function PhyloEM.

traits

a vector of integers giving the numbers of the trait to be plotted. Default to 1:p (all the traits).

params

(optional) some user-specified parameters. Must be of class params_process. If left blank, they are extracted using the method.selection argument (see below).

method.selection

select the parameters to plot. One of "LINselect", "DDSE", "Djump". Default to "LINselect". See params_process.PhyloEM.

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.

name_trait

name of the trait scale bar for the ancestral states plotting. Default to "Trait Value".

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_font

if show.tip.label=TRUE, the font of the labels (see par).

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.

axis_las

las for the label values of the plot. Default to 0 (see par).

show_axis_traits

control whether the trait values axis is plotted (default to TRUE).

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.

root.edge

a logical indicating whether to draw the root edge (defaults to TRUE)

...

further arguments to be passed to plot.phylo.

See also

params_process.PhyloEM, imputed_traits.PhyloEM