Create Term-Gene Plot

Source: R/visualize_term_gene_graph.R

Create Term-Gene Plot

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).

Value

A ggraph object

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.

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)