plot_heatmap: Plot Network as Heatmap

In cograph: Analysis and Visualization of Complex Networks

Plot Network as Heatmap

Description

Visualizes a network adjacency/weight matrix as a heatmap. Supports single networks, multi-cluster networks (block diagonal), and multi-layer networks (group_tna).

Usage

plot_heatmap(
  x,
  cluster_list = NULL,
  cluster_spacing = 0,
  show_legend = TRUE,
  legend_position = "right",
  legend_title = "Weight",
  colors = "viridis",
  limits = NULL,
  midpoint = NULL,
  na_color = "grey90",
  show_values = FALSE,
  value_size = 2.5,
  value_color = "black",
  value_fontface = "plain",
  value_fontfamily = "sans",
  value_halo = NULL,
  value_digits = 2,
  show_diagonal = TRUE,
  diagonal_color = NULL,
  cluster_labels = TRUE,
  cluster_borders = TRUE,
  border_color = "black",
  border_width = 0.5,
  row_labels = NULL,
  col_labels = NULL,
  show_axis_labels = TRUE,
  axis_text_size = 8,
  axis_text_angle = 45,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  threshold = 0,
  aspect_ratio = 1,
  ...
)

Arguments

x	Network input: matrix, CographNetwork, tna, igraph, group_tna, or any object cograph accepts.
cluster_list	Optional list of character vectors defining node clusters. Creates a block-structured heatmap with clusters along diagonal.
cluster_spacing	Gap size between clusters (in cell units). Default 0.
show_legend	Logical: display color legend? Default TRUE.
legend_position	Position: "right" (default), "left", "top", "bottom", "none".
legend_title	Title for legend. Default "Weight".
colors	Color palette: vector of colors for gradient, or a palette name ("viridis", "heat", "blues", "reds", "diverging"). Default "viridis".
limits	Numeric vector c(min, max) for color scale. NULL for auto.
midpoint	Midpoint for diverging scales. NULL for auto (0 if data spans neg/pos).
na_color	Color for NA values. Default "grey90".
show_values	Logical: display values in cells? Default FALSE.
value_size	Text size for cell values. Default 2.5.
value_color	Color for cell value text. Default "black".
value_fontface	Font face for values: "plain", "bold", "italic", "bold.italic". Default "plain".
value_fontfamily	Font family for values: "sans", "serif", "mono". Default "sans".
value_halo	Halo color behind value labels for readability on dark cells. Set to a color (e.g., "white") to enable, or NULL (default) to disable.
value_digits	Decimal places for values. Default 2.
show_diagonal	Logical: show diagonal values? Default TRUE.
diagonal_color	Optional color for diagonal cells. NULL uses scale.
cluster_labels	Logical: show cluster/layer labels? Default TRUE.
cluster_borders	Logical: draw borders around clusters? Default TRUE.
border_color	Color for cluster borders. Default "black".
border_width	Width of cluster borders. Default 0.5.
row_labels	Row labels. NULL for auto (rownames or indices).
col_labels	Column labels. NULL for auto (colnames or indices).
show_axis_labels	Logical: show axis tick labels? Default TRUE.
axis_text_size	Size of axis labels. Default 8.
axis_text_angle	Angle for x-axis labels. Default 45.
title	Plot title. Default NULL.
subtitle	Plot subtitle. Default NULL.
xlab	X-axis label. Default NULL.
ylab	Y-axis label. Default NULL.
threshold	Minimum absolute value to display. Values with abs(value) < threshold are set to zero. Default 0.
aspect_ratio	Aspect ratio. Default 1 (square cells).
...	Additional arguments (currently unused).

Details

For multi-cluster networks, provide cluster_list as a named list where each element is a vector of node names belonging to that cluster. The heatmap will be reordered to show clusters as blocks along the diagonal.

For group_tna objects (multiple separate networks), each network becomes a diagonal block. Off-diagonal blocks are empty (no inter-layer edges) unless the networks share nodes.

Value

A ggplot2 object.

Examples

## Not run: 
# Single network
m <- matrix(runif(25), 5, 5)
rownames(m) <- colnames(m) <- LETTERS[1:5]
plot_heatmap(m)

# With clusters
clusters <- list(Group1 = c("A", "B"), Group2 = c("C", "D", "E"))
plot_heatmap(m, cluster_list = clusters)

# Custom colors and legend
plot_heatmap(m, colors = "heat", limits = c(0, 1), show_values = TRUE)

## End(Not run)

## Not run: 
# Multi-layer (group_tna) — requires tna package and sequence data
if (requireNamespace("tna", quietly = TRUE)) {
  mod <- tna::tna(tna::group_regulation)
  plot_heatmap(mod)
}

## End(Not run)

cograph documentation built on April 1, 2026, 1:07 a.m.