cograph (version 2.7.2)

plot_mlna: Multilevel Network Visualization

Description

Visualizes multilevel/multiplex networks where multiple layers are stacked in a 3D perspective view. Each layer contains nodes connected by solid edges (within-layer), while dashed lines connect nodes between adjacent layers (inter-layer edges). Each layer is enclosed in a parallelogram shell giving a pseudo-3D appearance.

Usage

plot_mlna(
  model,
  layer_list = NULL,
  community = NULL,
  layout = "horizontal",
  layer_spacing = 4,
  layer_width = 8,
  layer_depth = 4,
  skew_angle = 25,
  node_spacing = 0.7,
  colors = NULL,
  shapes = NULL,
  edge_colors = NULL,
  within_edges = TRUE,
  between_edges = TRUE,
  between_style = 2,
  show_border = TRUE,
  legend = TRUE,
  legend_position = "topright",
  curvature = 0.15,
  node_size = 3,
  minimum = 0,
  scale = 1,
  show_labels = TRUE,
  nodes = NULL,
  label_abbrev = NULL,
  ...
)
mlna(
  model,
  layer_list = NULL,
  community = NULL,
  layout = "horizontal",
  layer_spacing = 4,
  layer_width = 8,
  layer_depth = 4,
  skew_angle = 25,
  node_spacing = 0.7,
  colors = NULL,
  shapes = NULL,
  edge_colors = NULL,
  within_edges = TRUE,
  between_edges = TRUE,
  between_style = 2,
  show_border = TRUE,
  legend = TRUE,
  legend_position = "topright",
  curvature = 0.15,
  node_size = 3,
  minimum = 0,
  scale = 1,
  show_labels = TRUE,
  nodes = NULL,
  label_abbrev = NULL,
  ...
)

Value

Invisibly returns NULL.

See plot_mlna.

Arguments

model

A tna object, weight matrix, or cograph_network.

layer_list

Layers can be specified as:

• A list of character vectors (node names per layer)

• A string column name from nodes data (e.g., "layer")

• NULL to auto-detect from columns named: layer, layers, groups, etc.

• NULL with community specified for algorithmic detection

community

Community detection method to use for auto-layering. If specified, overrides layer_list. See detect_communities for available methods: "louvain", "walktrap", "fast_greedy", "label_prop", "infomap", "leiden".

layout

Node layout within layers: "horizontal" (default) spreads nodes horizontally, "circle" arranges nodes in an ellipse, "spring" uses force-directed placement based on within-layer connections.

layer_spacing

Vertical distance between layer centers. Default 4.

layer_width

Horizontal width of each layer shell. Default 8.

layer_depth

Depth of each layer (for 3D effect). Default 4.

skew_angle

Angle of perspective skew in degrees. Default 25.

node_spacing

Node placement ratio within layer (0-1). Default 0.7. Higher values spread nodes closer to the layer edges.

colors

Vector of colors for each layer. Default auto-generated.

shapes

Vector of shapes for each layer. Default cycles through "circle", "square", "diamond", "triangle".

edge_colors

Vector of edge colors by source layer. If NULL (default), uses darker versions of layer colors.

within_edges

Logical. Show edges within layers (solid lines). Default TRUE.

between_edges

Logical. Show edges between adjacent layers (dashed lines). Default TRUE.

between_style

Line style for between-layer edges. Default 2 (dashed). Use 1 for solid, 3 for dotted.

show_border

Logical. Draw parallelogram shells around layers. Default TRUE.

legend

Logical. Whether to show legend. Default TRUE.

legend_position

Position for legend. Default "topright".

curvature

Edge curvature for within-layer edges. Default 0.15.

node_size

Size of nodes. Default 3.

minimum

Minimum edge weight threshold. Edges below this are hidden. Default 0.

scale

Scaling factor for spacing parameters. Use scale > 1 for high-resolution output (e.g., scale = 4 for 300 dpi). This multiplies layer_spacing, layer_width, and layer_depth to maintain proper proportions at higher resolutions. Default 1.

show_labels

Logical. Show node labels. Default TRUE.

nodes

Node metadata. Can be:

• NULL (default): Use existing nodes data from cograph_network

• Data frame: Must have label column for matching; if labels column exists, uses it for display text

Display priority: labels column > label column (identifiers).

label_abbrev

Label abbreviation: NULL (none), integer (max chars), or "auto" (adaptive based on node count).

...

Additional parameters (currently unused).

Examples

set.seed(42)
m <- matrix(runif(225, 0, 0.3), 15, 15); diag(m) <- 0
nodes <- paste0("N", 1:15)
colnames(m) <- rownames(m) <- nodes
layers <- list(Macro = nodes[1:5], Meso = nodes[6:10], Micro = nodes[11:15])
plot_mlna(m, layers)
# \donttest{
plot_mlna(m, layers, layout = "circle", between_style = 2, minimum = 0.1)
# }
set.seed(1)
nodes <- paste0("N", 1:9)
m <- matrix(runif(81, 0, 0.3), 9, 9); diag(m) <- 0
colnames(m) <- rownames(m) <- nodes
layers <- list(L1 = nodes[1:3], L2 = nodes[4:6], L3 = nodes[7:9])
mlna(m, layers)