# Script for dot plot generation

organism = "org.Hs.eg.db"
BiocManager:: install(organism, character.only = TRUE)
library(organism, character.only = TRUE)
library(clusterProfiler)

# Reding input file with DEGs
df = read.csv("input_genes.csv", header = TRUE)
original_gene_list <- df$log2FC
names(original_gene_list) <- df$SYMBOL

gene_list <- na.omit(original_gene_list)
gene_list = sort(gene_list, decreasing = TRUE)

# Running gene set enrichment 
gse <- gseGO(geneList = gene_list, ont = "ALL", keyType = "SYMBOL", nPerm = 10000, minGSSize = 3, maxGSSize = 500, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = "org.Hs.eg.db", pAdjustmethod = "BH")

# Making dotplot
dotplot(gse, showCategory = 20)

