plot.Knowledge: Plot a Knowledge Object

In causalDisco: Tools for Causal Discovery on Observational Data

Plot a Knowledge Object

Description

Visualize a Knowledge object as a directed graph using caugi::plot().

Usage

## S3 method for class 'Knowledge'
plot(x, required_col = "blue", forbidden_col = "red", ...)

Arguments

x	A Knowledge object, created using knowledge().
required_col	Character(1). Color for edges marked as "required". Default "blue".
forbidden_col	Character(1). Color for edges marked as "forbidden". Default "red".
...	Additional arguments passed to caugi::plot(), e.g., node_style, edge_style.

Details

• Required edges are drawn in blue by default (can be changed via required_col).

• Forbidden edges are drawn in red by default (can be changed via forbidden_col). If A to B and B to a is forbidden, a edge ⁠<->⁠ is drawn.

• If tiered knowledge is provided, nodes are arranged according to their tiers.

• Users can override other edge styling (e.g., line width, arrow size) via the edge_style argument. To override the color of a specific edge, use edge_style$by_edge[[from]][[to]]$col.

• Nodes are arranged by tiers if tier information is provided in the Knowledge object.

• If some nodes are missing tier assignments, a warning is issued and the plot falls back to untiered plotting.

• The function automatically handles edges marked as "required" or "forbidden" in the Knowledge object.

• Other edge styling (line width, arrow size, etc.) can be supplied via edge_style. The only way to override edge colors for specific edges is to specify them directly in edge_style$by_edge[[from]][[to]]$col.

Value

Invisibly returns the caugi::caugi object used for plotting. The main effect is the plot.

Examples

data(tpc_example)

# Define a `Knowledge` object with tiers
kn_tiered <- knowledge(
  tpc_example,
  tier(
    child ~ starts_with("child"),
    youth ~ starts_with("youth"),
    old ~ starts_with("old")
  )
)

# Simple plot (default column orientation)
plot(kn_tiered)

# Plot with row orientation
plot(kn_tiered, orientation = "rows")

# Plot with custom node styling, edge width/arrow size and edge colors
kn <- knowledge(
  tpc_example,
  tier(
    child ~ starts_with("child"),
    youth ~ starts_with("youth"),
    old ~ starts_with("old")
  ),
  child_x1 %-->% child_x2, # required edge
  youth_x4 %!-->% youth_x3  # forbidden edge
)
plot(
  kn,
  node_style = list(
    fill = "lightblue", # Fill color
    col = "darkblue", # Border color
    lwd = 2, # Border width
    padding = 4, # Text padding (mm)
    size = 1.2 # Size multiplier
  ),
  edge_style = list(
    lwd = 1.5, # Edge width
    arrow_size = 4 # Arrow size (mm)
  ),
  required_col = "darkgreen",
  forbidden_col = "darkorange"
)

# To override a specific edge style which is required/forbidden
# you need to target that individual node:
kn <- knowledge(
  tpc_example,
  tier(
    child ~ starts_with("child"),
    youth ~ starts_with("youth"),
    old ~ starts_with("old")
  ),
  child_x1 %-->% c(child_x2, youth_x4), # required edges
  youth_x4 %!-->% c(youth_x3, oldage_x5)  # forbidden edges
)

# Edge from child_x1 to child_x2 will be orange, but edge from child_x1 to youth_x4
# will be required_col (blue) since we only override the child_x1 to child_x2 edge.
# Similarly, edge from youth_x4 to youth_x3 will be yellow, but edge from youth_x4
# to oldage_x5 will be forbidden_col (red).
plot(
  kn,
  edge_style = list(
    by_edge = list(
      child_x1 = list(
        child_x2 = list(col = "orange", fill = "orange")
      ),
      youth_x4 = list(
        youth_x3 = list(col = "yellow", fill = "yellow")
      )
    )
  ),
  required_col = "blue",
  forbidden_col = "red"
)

# Define a `Knowledge` object without tiers
kn_untiered <- knowledge(
  tpc_example,
  child_x1 %-->% c(child_x2, youth_x3),
  youth_x4 %!-->% oldage_x5
)
# Plot with default layout
plot(kn_untiered)

# With a custom defined layout
custom_layout <- data.frame(
 name = c("child_x1", "child_x2", "youth_x3", "youth_x4", "oldage_x5", "oldage_x6"),
 x = c(0, 1, 2, 2, 3, 4),
 y = c(0, 1, 0, -1, 0, 1)
)
plot(kn_untiered, layout = custom_layout)

causalDisco documentation built on April 13, 2026, 5:06 p.m.