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Create an interactive visualization of KEGG pathways with visNetwork

Source: R/network_operations.R
render_kegg_graph.Rd

Plot KEGG pathway graph using visNetwork

Usage

render_kegg_graph(
  g,
  graph_title = NULL,
  scaling_factor = 1.5,
  relationships = c("all", "reactions", "relations", "none"),
  visualization_type = c("standard", "positions", "node_name", "node_size")
)

Arguments

g

An igraph object representing the KEGG pathway graph.

graph_title

Character string, used as a title for the rendered graph. Defaults to NULL, which would fall back to the name specified in the title attribute of the graph.

scaling_factor

Numeric factor to scale node sizes (default: 1.5).

relationships

Character specifying which relationships to include in edges ("all", "reactions", "relations", "none"; default: "all").

visualization_type

Character specifying the type of visualization for nodes: "standard", "positions", "node_name", or "node_size" (default: "standard").

Value

A visNetwork object representing the KEGG pathway graph with mapped results.

Details

This function takes an igraph object representing a KEGG pathway graph and creates a visNetwork visualization. It maps node attributes to visual properties.

Examples

pathway <- "hsa04110" # Example pathway ID
graph <- create_kegg_graph(pathway_id = pathway)
# Example differential expression results
de_results <- data.frame(
  KEGG_ids = c("hsa:1234", "hsa:5678", "cpd:C00022"),
  log2FoldChange = c(1.5, -2.0, 0.5)
)
graph <- map_results_to_graph(
  graph,
  de_results,
  feature_column = "KEGG_ids",
  value_column = "log2FoldChange")
#> de_results provided as a single data.frame. Using provided value_column: 'log2FoldChange' and feature_column: 'KEGG_ids'.

vis_graph <- render_kegg_graph(graph, scaling_factor = 1.5,
relationships = "all", visualization_type = "standard")