Hey mates,

My script is running perfectly and produces an graph with the genes connected to each other and the pathways. However, now I would like to remove the pathways connection and only have the genes connected to each other.

Here is a sample functioning code that resembles my script;

install.packages(BiocManager)
BiocManager::install("ReactomePA",force = TRUE)
install.packages(c("igraph","dplyr"))
library(ReactomePA)
library(igraph)

random_genes <- c("11171", "8243", "112464", "2194", "9318", "79026", "1654", "65003",
            "6240", "3476", "6238", "3836", "4176", "1017", "249")

# Pathway enrichment analysis
enriched_pathways <- enrichPathway(gene = random_genes, organism = "mouse")

# Extract pathway and gene information
pathways <- as.data.frame(enriched_pathways)

`# Create an edge list for the graph
edge_list <- data.frame(
  from = rep(pathways$Description, each = length(genes)),
  to = rep(genes, times = nrow(pathways)))

# Excluding NON-hallmark pathways [IS THIS STILL NEEDED]
exclude_pathway <- c("Biological oxidations","Arachidonic acid metabolism",
                    "Platelet homeostasis","Paracetamol ADME","Fatty acid metabolism")

# # Removing pathways not in my interest
 edge_list<-edge_list %>% dplyr::filter(!(from %in% exclude_pathway)) 

# Graph & Results ------------------------------------------------------------------

# Create the graph
g <- graph_from_data_frame(edge_list, directed = FALSE)

# Setting my layout preference
layout<-layout_with_graphopt(g) #drl w/ vertex size 3 looks the best
                                #graphopt w/ vertex size 1 is next best

# The graph
plot(g, layout = layout, vertex.label.cex = 0.8, 
vertex.size = 3, vertex.label.dist = 0.5)

Thank you all, I solved my issue by creating a for loop.

Cheers!