Plot method for multilayer MixMashNet objects

Plotting interface for objects returned by multimixMN().

Depending on what, the method can:

• what = "network": plot the estimated multilayer network, or a single layer if layer is specified;

• what = "intra": plot intralayer node-level metrics or edge weights with bootstrap quantile regions;

• what = "inter": plot interlayer node metrics or interlayer edge weights with bootstrap quantile regions;

• what = "stability": plot node stability within communities based on bootstrap community assignments.

Usage

# S3 method for class 'multimixMN_fit'
plot(x, what = c("network", "intra", "inter", "stability"), layer = NULL, ...)

Arguments

x

An object of class "multimixMN_fit", as returned by multimixMN().

what

Type of plot to produce. One of c("network","intra","inter","stability").

layer

Optional layer name. For what = "intra" or what = "stability", this selects which layer-specific fit to use. For what = "network", if provided, the selected layer is plotted as a single layer network.

...

Additional arguments. Supported arguments depend on what: see the details below.

Value

If what != "network", the function returns a ggplot object. If what = "network", the network is plotted directly.

Details

Network plots (what = "network"): Supported arguments (via ...):

color_by

Node coloring: c("layer","community","none").

edge_color_by

Edge coloring: c("sign","none").

edge_scale

Numeric scaling factor for edge widths (multiplied by abs(weight)).

graphics::plot.igraph arguments

e.g., vertex.size, vertex.label.cex, edge.width, vertex.label.color, etc.

Intralayer statistics (what = "intra"): Plots node-level metrics or edge weights with bootstrap quantile regions. If layer is provided, only that layer is plotted. If layer is NULL, all layers are plotted, one panel per layer.

Supported arguments (via ...):

statistics

Character vector of metrics. Options include: "strength", "expected_influence", "closeness", "betweenness", bridge metrics "bridge_strength", "bridge_ei1", "bridge_ei2", "bridge_closeness", "bridge_betweenness", excluded bridge metrics "bridge_strength_excluded", "bridge_ei1_excluded", "bridge_ei2_excluded", "bridge_closeness_excluded", "bridge_betweenness_excluded", and "edges". Different metric families cannot be mixed in the same call (e.g., "edges" cannot be combined with node metrics).

ordering

Node ordering: c("value","alphabetical","community").

standardize

Logical; if TRUE, z-standardize the displayed values within each panel.

exclude_nodes

Optional character vector of node names to remove before plotting.

color_by_community

Logical; if TRUE, color nodes by community when available.

edges_top_n

Integer; when statistics = "edges", keep the top edges by absolute weight.

title

Optional plot title. If omitted and multiple layers are shown, layer-specific titles are added automatically.

Interlayer summaries (what = "inter"): Plots interlayer node metrics or interlayer edge weights with bootstrap quantile regions.

Supported arguments (via ...):

statistics

Character vector. Node metrics: c("strength","expected_influence","closeness","betweenness"), or "edges" for interlayer edge weights. Node metrics and "edges" cannot be combined.

pairs

Layer pairs to show. Either "*" (all available) or a character vector of pair keys like "bio_dis" (order-insensitive).

edges_top_n

Integer; keep the top interlayer edges by absolute weight.

ordering

Ordering within panels: c("value","alphabetical").

standardize

Logical; if TRUE, z-standardize values (node metrics by metric, edges by pair).

exclude_nodes

Optional character vector; removes nodes and incident interlayer edges.

nodes_layer

Optional layer name to restrict node metrics to nodes belonging to that layer.

title

Optional plot title.

Community membership stability (what = "stability"): Plots node stability by community. If layer is provided, only that layer is shown. Otherwise, stability plots are shown for all layers.

Supported arguments (via ...):

title

Plot title. Default: "Node Stability by Community".

cutoff

Optional numeric threshold in \([0,1]\) shown as a dashed vertical line. Use NULL to hide the line. Default: 0.7.

The quantile region level is taken from the fitted object (x$settings$quantile_level); if missing or invalid, a default of 0.95 is used.

See also

multimixMN