Entering edit mode
20 months ago
sharmatina189059
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110
BiocManager::install("clusterProfiler", version = "3.16")
BiocManager::install("pathview")
BiocManager::install("enrichplot")
library(clusterProfiler)
library(enrichplot)
# we use ggplot2 to add x axis labels (ex: ridgeplot)
library(ggplot2)
# reading in data from deseq2
df = read.csv("C:/DE_gene_downregulated_clusterprofiler.csv", header=TRUE)
View(df)
organism = "org.Hs.eg.db" #set the desired organism here, # org.Hs.eg.db for human
BiocManager::install(organism, character.only = TRUE)
library(organism, character.only = TRUE)
# we want the log2 fold change
original_gene_list <- df$PostFC
original_gene_list
# name the vector
names(original_gene_list) <- df$X
# omit any NA values
gene_list<-na.omit(original_gene_list)
# sort the list in decreasing order (required for clusterProfiler)
gene_list = sort(gene_list, decreasing = TRUE)
gene_list
gse <- gseGO(geneList=gene_list,
ont ="BP",
keyType = "ENSEMBL",
minGSSize = 1,
maxGSSize = 450,
pvalueCutoff = 0.05,
verbose = TRUE,
OrgDb = organism,
pAdjustMethod = "none")
cluster_summary <- data.frame(gse)
write.csv(cluster_summary, "C:/DE_gene/clusterProfiler_out.csv")
require(DOSE)
dotplot(gse, showCategory=10, orderBy = "setSize", split=".sign") + facet_grid(.~.sign)