combined_results_graph: Combined Results Graph

In egeulgen/pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Combined Results Graph

Description

Combined Results Graph

Usage

combined_results_graph(
  combined_df,
  selected_terms = "common",
  use_description = FALSE,
  layout = "stress",
  node_size = "num_genes"
)

Arguments

combined_df	Data frame of combined pathfindR enrichment results
selected_terms	the vector of selected terms for creating the graph (either IDs or term descriptions). If set to 'common', all of the common terms are used. (default = 'common')
use_description	Boolean argument to indicate whether term descriptions (in the 'Term_Description' column) should be used. (default = FALSE)
layout	The type of layout to create (see ggraph for details. Default = 'stress')
node_size	Argument to indicate whether to use number of significant genes ('num_genes') or the -log10(lowest p value) ('p_val') for adjusting the node sizes (default = 'num_genes')

Value

a ggraph object containing the combined term-gene graph. Each node corresponds to an enriched term (orange if common, different shades of blue otherwise), an up-regulated gene (green), a down-regulated gene (red) or a conflicting (i.e. up in one analysis, down in the other or vice versa) gene (gray). An edge between a term and a gene indicates that the given term involves the gene. Size of a term node is proportional to either the number of genes (if node_size = 'num_genes') or the -log10(lowest p value) (if node_size = 'p_val').

Examples

combined_results <- combine_pathfindR_results(
  example_pathfindR_output,
  example_comparison_output,
  plot_common = FALSE
)
g <- combined_results_graph(combined_results, selected_terms = sample(combined_results$ID, 3))

egeulgen/pathfindR documentation built on Feb. 1, 2024, 4:34 a.m.