Plot Network as Heatmap — plot

Visualizes a network weight matrix as a heatmap. Single networks, clustered networks (blocks along the diagonal), and multi-group networks (group_tna, as a supra-adjacency matrix) are supported.

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, cograph_network, tna, igraph, group_tna, or a list-like object with a $weights matrix.
cluster_list: Optional list of character vectors of node names defining node clusters. The matrix is reordered so that clusters form blocks along the diagonal. Nodes not listed are dropped, and a listed name that is not in the matrix is an error.
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: a vector of colors for the gradient, a palette name ("viridis", "heat", "blues", "reds", "greens", "diverging"), or a single color name, which gives a gradient from white to that color. With a diverging scale the first three colors are used as low, mid and high. Two colors are used as low and high around a white midpoint, and a single color name is used as the high end, with the blue low end and the light gray midpoint of the "diverging" palette. Default "viridis".
limits: Numeric vector c(min, max) for color scale. NULL for auto.
midpoint: Midpoint of a diverging scale. Supplying it makes the scale diverging. With the default NULL, the scale is diverging around 0 when the values span negative and positive numbers.
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: Currently unused. Diagonal cells use the fill scale unless they are hidden with show_diagonal = FALSE.
cluster_labels: Logical: show cluster or group labels? With a cluster_list, labels are shown only when the list is named. For group_tna input the group names are shown. Default TRUE.
cluster_borders: Logical: plot 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 for a single-network heatmap. NULL uses the row names or indices.
col_labels: Column labels for a single-network heatmap. NULL uses the column names or indices.
show_axis_labels: Logical: show axis tick labels? Default TRUE. A clustered heatmap never shows axis tick labels.
axis_text_size: Size of axis labels. Default 8.
axis_text_angle: Angle for x-axis labels. Default 45.
title: Plot title. Default NULL, which gives no title, or "Supra-Adjacency Heatmap" for group_tna input.
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. It is not applied to group_tna input. Default 0.
aspect_ratio: Aspect ratio. Default 1 (square cells).
...: Additional arguments (currently unused).

Value

A ggplot object.

Details

For group_tna objects, each group network becomes a diagonal block of a supra-adjacency matrix, with cells labelled group:node. The off-diagonal blocks are NA and take na_color. The node labels are taken from the first group.

Examples

plot_heatmap(regulation_net)