Create a Graph w/ Only the Genes Interaction
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Entering edit mode
Antonio • 0
@44ee1e1d
Last seen 15 days ago
United States

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)
EnrichedPathways GeneInteractionGraph graph • 143 views
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0
Entering edit mode
Antonio • 0
@44ee1e1d
Last seen 15 days ago
United States

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

Cheers!

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