cograph (version 2.0.0)

plot_heatmap: 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,
  ...
)

Value

A ggplot2 object.

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.

Examples

if (FALSE) {
# 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)
}

if (FALSE) {
# Multi-layer (group_tna) — requires tna package and sequence data
if (requireNamespace("tna", quietly = TRUE)) {
  mod <- tna::tna(tna::group_regulation)
  plot_heatmap(mod)
}
}