create_term_gene_plot: Create Term-Gene Plot

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Create Term-Gene Plot

Description

Create Term-Gene Plot

Usage

create_term_gene_plot(
  graph,
  layout = "stress",
  gene_node_fill = c("#7E2795", "white", "#27AE60"),
  term_node_fill = c("#CCBB44", "white", "#4477AA"),
  gene_node_color = c("green", "red"),
  term_node_color = "#E5D7BF",
  term_fill_label = NULL,
  term_size_label = NULL
)

Arguments

graph	A igraph returned from create_term_gene_graph.
layout	The type of layout to create (see ggraph for details (default: 'stress')
gene_node_fill	A character vector to customize the fill gradient colors of the gene nodes when 'genes_df' is supplied, color order is in low -> mid -> high (default: c("#7E2795", "white", "#27AE60")).
term_node_fill	A character vector to customize the fill gradient colors of the term nodes when 'term_fill' is supplied, color order is in low -> mid -> high (default: c("#CCBB44", "white", "#4477AA")).
gene_node_color	A character vector to customize the fill gradient colors of the term nodes when 'genes_df' is not supplied, color order is in up -> down (default: c("green", "red")).
term_node_color	A character to customize the fill color of the terms when 'term_fill' is not specified (default: "#E5D7BF").
term_fill_label	A character to change the term node legend name (default: NULL).
term_size_label	A character to change the term node size legend name (default: NULL).

Details

This function creates a visualization of the term-gene graph (adapted from the Gene-Concept network visualization in the enrichplot package). It displays which input genes are involved in enriched biological terms, showing connections between genes and pathway/terms nodes. The graph facilitates investigation of multi-term relationships and identifies shared versus distinct genes across enriched terms.

Node coloring depends on the inputs provided to create_term_gene_graph:

• If 'genes_df' was NOT supplied: term nodes are beige ('term_node_color'), up-regulated genes are green, and down-regulated genes are red.

• If 'genes_df' WAS supplied: gene nodes are colored by logFC using a gradient ('gene_node_fill': default purple → white → green), and term nodes can be colored by 'term_fill' values (default yellow → white → blue) if 'term_fill' was provided.

Term node size reflects either the number of associated genes (‘term_size = ’num_genes'‘) or statistical significance ('term_size = ’p_val''). When 'use_edge_weights = TRUE' was set in 'create_term_gene_graph', edge widths represent hub gene importance (genes appearing in multiple terms). The layout can be customized via the 'layout' parameter (default: "stress"), and legends automatically reflect the applied coloring schemes.

Value

A ggraph object

Examples

# Normal gene-term with up/down regulated genes
g <- create_term_gene_graph(
  result_df = example_pathfindR_output
)
plt <- create_term_gene_plot(g)

pathfindR documentation built on July 2, 2026, 1:06 a.m.