Plot a Local Network Around a Target Node from tKOI Results

Draws the part of the knowledge graph that links a target node (for example an enriched GO term) to the significant genes near it. Genes are colored by log fold change (blue down, white zero, red up), the target is orange, other nodes are gray, and node size follows the tKOI effect size (beta).

Usage

plot_network(
  tkoi_result,
  target_node_id,
  degree_expansion = 2,
  network_layout_type = c("kk", "fr", "gem", "graphopt", "lgl", "mds"),
  subnetwork = NULL
)

Arguments

tkoi_result

A tKOIList returned by run_tkoi.

target_node_id

Node ID (vertex name) of the node to center on.

degree_expansion

Maximum number of hops between the target and a gene. Default 2.

network_layout_type

Layout algorithm: "kk" (Kamada-Kawai, the default), "fr" (Fruchterman-Reingold), "gem", "graphopt", "lgl", or "mds".

subnetwork

The igraph network used for the analysis. When NULL, uses the graph retained in tkoi_result via get_analysis_graph(). For older results without a stored graph, supply the original analysis graph explicitly.

Value

The plotted igraph subgraph, invisibly.

Details

Significant genes pass the p-value and log fold change thresholds stored in tkoi_result. The plot shows every node on a simple path of at most degree_expansion edges between the target and one of these genes. For degree_expansion <= 2 these nodes are found directly from neighbor sets; longer paths use igraph::all_simple_paths(), which can be slow around highly connected nodes.

Examples

if (FALSE) { # \dontrun{
top_term = tkoi_result@network_summary_statistics$BiologicalProcess$node_id[1]
plot_network(tkoi_result, target_node_id = top_term, degree_expansion = 2)
} # }