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Plot Network Graph of Features or Exposures

Source: R/plot_network.R
plot_network.Rd

Visualizes network structures created by run_create_network() from the metadata of a MultiAssayExperiment object. Nodes can represent features (e.g., genes or factors) or exposures, and edges represent correlations or shared connections.

Usage

plot_network(
  expomicset,
  network = c("degs", "omics", "factors", "factor_features", "exposures",
    "degs_feature_cor", "omics_feature_cor", "factor_features_feature_cor"),
  include_stats = TRUE,
  nodes_to_include = NULL,
  centrality_thresh = NULL,
  top_n_nodes = NULL,
  cor_thresh = NULL,
  label = FALSE,
  label_top_n = 5,
  nodes_to_label = NULL,
  facet_var = NULL,
  foreground = "steelblue",
  fg_text_colour = "grey25",
  node_colors = NULL,
  node_color_var = NULL,
  alpha = 0.5,
  size_lab = "Centrality",
  color_lab = "Group"
)

Arguments

expomicset

A MultiAssayExperiment object containing network results in metadata.

network

Character string specifying the network type. One of "degs", "omics", "factors", "factor_features", "exposures", "degs_feature_cor", "omics_feature_cor", "factor_features_feature_cor".

include_stats

Logical; if TRUE, include edge weights and node centrality metrics in the plot aesthetics. Default is TRUE.

nodes_to_include

Optional character vector of node names to include (subset of name).

centrality_thresh

Optional numeric threshold to filter nodes by centrality degree.

top_n_nodes

Optional integer to keep only the top N nodes by centrality.

cor_thresh

Optional numeric threshold to filter edges by minimum absolute correlation.

label

Logical; whether to label nodes. If TRUE, top nodes will be labeled.

label_top_n

Integer; number of top-centrality nodes to label if label = TRUE. Default is 5.

nodes_to_label

Optional character vector of specific nodes to label.

facet_var

Optional node metadata column to facet the network layout by.

foreground

Color for node outlines and edge borders. Default is "steelblue".

fg_text_colour

Color of node label text. Default is "grey25".

node_colors

Optional named vector of colors for node groups.

node_color_var

Optional node attribute used for node color mapping.

alpha

Alpha transparency for nodes and edges. Default is 0.5.

size_lab

Legend title for node size (typically centrality). Default is "Centrality".

color_lab

Legend title for node color group. Default is "Group".

Value

A ggraph plot object.

Details

This function retrieves the stored graph object and optionally filters or labels nodes based on: centrality, correlation, user input, or group-specific attributes. It supports layout faceting, custom color mappings, and highlights highly central nodes.

Large graphs (> 500 nodes) will prompt the user before plotting.

Examples

if (FALSE) { # \dontrun{
plot_network(expomicset, network = "degs", label = TRUE)
plot_network(expomicset, network = "exposures", cor_thresh = 0.4)
plot_network(expomicset, network = "omics", top_n_nodes = 50, node_color_var = "exp_name")
} # }