term_gene_graph {pathfindR}

Create Term-Gene Graph

Description

Create Term-Gene Graph

Usage

term_gene_graph(
  result_df,
  num_terms = 10,
  layout = "stress",
  use_description = FALSE,
  node_size = "num_genes",
  node_colors = c("#E5D7BF", "green", "red")
)

Arguments

result_df

A dataframe of pathfindR results that must contain the following columns:

Term_Description

Description of the enriched term (necessary if use_description = TRUE)

ID

ID of the enriched term (necessary if use_description = FALSE)

lowest_p

the lowest adjusted-p value of the given term over all iterations

Up_regulated

the up-regulated genes in the input involved in the given term's gene set, comma-separated

Down_regulated

the down-regulated genes in the input involved in the given term's gene set, comma-separated

num_terms

Number of top enriched terms to use while creating the graph. Set to NULL to use all enriched terms (default = 10, i.e. top 10 terms)

layout

The type of layout to create (see ggraph for details. Default = 'stress')

use_description

Boolean argument to indicate whether term descriptions (in the 'Term_Description' column) should be used. (default = FALSE)

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')

node_colors

vector of 3 colors to be used for coloring nodes (colors for term nodes, up, and down, respectively)

Details

This function (adapted from the Gene-Concept network visualization by the R package enrichplot) can be utilized to visualize which input genes are involved in the enriched terms as a graph. The term-gene graph shows the links between genes and biological terms and allows for the investigation of multiple terms to which significant genes are related. The graph also enables determination of the overlap between the enriched terms by identifying shared and distinct significant term-related genes.

Value

a ggraph object containing the term-gene graph. Each node corresponds to an enriched term (beige), an up-regulated gene (green) or a down-regulated gene (red). 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

p <- term_gene_graph(example_pathfindR_output)
p <- term_gene_graph(example_pathfindR_output, num_terms = 5)
p <- term_gene_graph(example_pathfindR_output, node_size = 'p_val')