Plot method for MixMashNet objects — plot.mixmashnet • MixMashNet

Unified plotting interface for objects returned by mixMN() and multimixMN(). Depending on what, it can:

what = "network": plot the estimated network (single layer or multilayer);
what = "intra": plot intralayer node/edge statistics with bootstrap quantile regions at the level stored in the object (centrality and bridge metrics);
what = "inter": plot interlayer node metrics or interlayer edge weights with bootstrap quantile regions at the level stored in the object (multilayer only), and the chosen statistics;
what = "stability": plot node stability within communities based on bootstrap community assignments.

Usage

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

Arguments

x: An object of class mixmashnet, as returned by mixMN() or multimixMN().
what: Type of plot to produce. One of c("network","intra","inter","stability").
layer: Optional layer name. For what = "intra" or what = "stability" on a multimixMN_fit object, this selects which layer-specific fit to use.
...: 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. Single layer: c("community","none"). Multilayer: 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. For multilayer objects:

if layer is provided, plots that layer only;
if layer is NULL, plots all layers (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". Note: 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. In multilayer mode, if not provided a layer-specific title is added automatically.

Interlayer summaries (what = "inter"; multilayer only): 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. For multilayer objects, layer selects a specific layer; if layer is NULL, 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.