plot_difference: Plot Network Difference

In cograph: Analysis and Visualization of Complex Networks

Plot Network Difference

Description

Plots the difference between two networks (x - y) using splot. Positive differences (x > y) are shown in green, negative (x < y) in red. Optionally displays node-level differences (e.g., initial probabilities) as donut charts.

Usage

plot_difference(
  x,
  y = NULL,
  i = NULL,
  j = NULL,
  pos_color = "#009900",
  neg_color = "#C62828",
  labels = NULL,
  title = NULL,
  inits_x = NULL,
  inits_y = NULL,
  show_inits = NULL,
  donut_inner_ratio = 0.8,
  force = FALSE,
  combined = TRUE,
  difference = FALSE,
  ...
)

Arguments

x	First network: matrix, cograph_network, CographNetwork, tna, igraph, list-like object with $weights, plain list of networks, or group_tna. For group_tna with 2 groups, compares them directly. For more groups, plots all pairwise comparisons (or specify i, j).
y	Second network: same type as x. Ignored if x is a list or group_tna.
i	Index/name of first group when x is group_tna or a plain list. NULL plots all pairs for a group_tna of more than two groups, and selects the first element otherwise.
j	Index/name of second group when x is group_tna or a plain list. NULL plots all pairs for a group_tna of more than two groups, and selects the second element otherwise.
pos_color	Color for positive differences (x > y). Default "#009900" (green).
neg_color	Color for negative differences (x < y). Default "#C62828" (red).
labels	Node labels. NULL uses rownames or defaults.
title	Plot title. NULL for auto-generated title.
inits_x	Node values for x (e.g., initial probabilities). NULL to auto-extract from tna.
inits_y	Node values for y. NULL to auto-extract from tna.
show_inits	Logical: show node differences as donuts? Default NULL, which shows them when inits are available for both networks.
donut_inner_ratio	Inner radius ratio for donut (0-1). Default 0.8.
force	Logical: force plotting when more than 4 groups (many comparisons). Default FALSE.
combined	Logical: when TRUE (default) and x is a multi-group input that triggers all-pairs plotting, lay panels out in an internal grid via graphics::par(mfrow=...). Set to FALSE to draw into a layout the caller has already configured (e.g. via panel_layout()). Has no effect for the single-pair path.
difference	Logical. If TRUE, x is treated as an already-subtracted difference network (no y needed). A tna_comparison object (from tna::compare()) is detected automatically and its $difference_matrix is used.
...	Additional arguments passed to splot().

Details

The function computes element-wise subtraction of the weight matrices. Edge colors indicate direction of difference:

• Green edges: x has higher weight than y

• Red edges: y has higher weight than x

When initial probabilities (inits) are provided or extracted from tna objects, nodes display donut charts showing the absolute difference, colored by direction:

• Green donut: x has higher initial probability

• Red donut: y has higher initial probability

For lists of networks (e.g., group_tna), specify which elements to compare using i and j parameters.

Value

Invisibly returns a list with elements weights (the element-wise difference matrix x - y) and inits (the node-value difference, or NULL when no inits were available). For the group_tna all-pairs path, a named list of such lists — one element per pair, named "<group_i>_vs_<group_j>".

See Also

plot_compare, a first-class alias of this function kept for the tna integration. plot_difference() is the preferred name.

Examples

set.seed(42)
m1 <- matrix(runif(25), 5, 5)
m2 <- matrix(runif(25), 5, 5)
rownames(m1) <- colnames(m1) <- LETTERS[1:5]
rownames(m2) <- colnames(m2) <- LETTERS[1:5]
plot_difference(m1, m2)

# With node-level differences
plot_difference(m1, m2,
                inits_x = c(.3, .2, .2, .15, .15),
                inits_y = c(.1, .4, .2, .2, .1))

cograph documentation built on Sept. 30, 2026, 5:08 p.m.