phylopath (version 1.2.1)

plot.fitted_DAG: Plot a directed acyclic graph with path coefficients.

Description

Plot a directed acyclic graph with path coefficients.

Usage

# S3 method for fitted_DAG
plot(
  x,
  type = "width",
  labels = NULL,
  algorithm = "sugiyama",
  manual_layout = NULL,
  text_size = 6,
  box_x = 12,
  box_y = 8,
  edge_width = 1.25,
  curvature = 0.02,
  rotation = 0,
  flip_x = FALSE,
  flip_y = FALSE,
  arrow = grid::arrow(type = "closed", 18, grid::unit(15, "points")),
  colors = c("firebrick", "navy"),
  show.legend = TRUE,
  width_const = NULL,
  ...
)

Arguments

x

An object of class fitted_DAG.

type

How to express the weight of the path. Either "width", or "color".

labels

An optional set of labels to use for the nodes. This should be a named vector, of the form c(var1 = "label1", var2 = "label2"). If left at `NULL``, the variable names of the DAGs are used.

algorithm

A layout algorithm from igraph, see ggraph::create_layout(). By default, uses the Sugiyama layout algorithm, which is designed to minimize edge crossing in DAGs.

manual_layout

Alternatively, precisely define the layout yourself, by providing a data.frame that at least has a column name with all variable names, and columns x and y with positions to be plotted. Setting this parameter overrides algorithm but other changes, such as rotation and flips will still be applied.

text_size

Size of the node label text.

box_x

To avoid the arrows colliding with the nodes, specify the rectangular dimensions of an invisible box around each node. If you have long labels, you need to increase this.

box_y

To avoid the arrows colliding with the nodes, specify the rectangular dimensions of an invisible box around each node. If you have multi-line labels, you need to increase this.

edge_width

Width of the edges.

curvature

Curvature of the edges. A slight curvature can look pretty.

rotation

Supply the degrees you want to rotate the layout by. This is useful in order to put rotate your upstream nodes towards the top if needed.

flip_x

Whether to flip the node positions horizontally.

flip_y

Whether to flip the node positions vertically.

arrow

A grid::arrow object, specifying the shape and size of the arrowheads.

The order of facets is taken from the ordering of the list, with the facet labels coming from the names of the list. If the list is unnamed, sequential lettering is used.

colors

The end points of the continuous color scale. Keep in mind that red and green are obvious colors to use, but are better to be avoided because of color blind users.

show.legend

Whether a legend for the color scale should be shown.

width_const

Deprecated.

...

Not used.

Examples

  d <- DAG(LS ~ BM, NL ~ BM, DD ~ NL + LS)
  d_fitted <- est_DAG(d, rhino, rhino_tree, 'lambda')
  plot(d_fitted)