Enrich_plot: Enrich plot for GO terms and pathways.

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Enrich plot for GO terms and pathways.

Description

This function outputs the groups, GO terms and pathways plot for the enrichment based on R package clusterProfiler and org.Mm.eg.db (Mouse for example).

Usage

Enrich_plot(
  regiongenealls_significant,
  adjustpvaluecut = 0.1,
  enrichterm = "pathway",
  category = TRUE,
  Dbannotation = "org.Mm.eg.db",
  keggorganism = "mmu",
  listnum = 20,
  title = "Enrichment for significant gene",
  expressionfile_significant = NULL,
  expressionfile_genetype = NULL
)

Arguments

regiongenealls_significant	refers to the differentially methylated genes.
adjustpvaluecut	refers to the threshold of the adjusted P values for the enrichment, with default 0.1.
enrichterm	refers to the term need to be analyzed, which can be "GOgroup", "GO", "pathway", with default "pathway".
category	refers to whether to divide the enrichments into two categories, i.e., hypo/hyper methylated or down/up regulated, with default TRUE.
Dbannotation	refers to the annotation dataset, with default "org.Mm.eg.db" of mouse.
keggorganism	refers to the species name for KEGG enrichment, with default "mmu" of mouse.
listnum	refers to the list of display number, with default 20.
title	refers to the title of figure, with default "Enrichments for significant gene".
expressionfile_significant	refers to an additional file for differentially expressed genes which includes gene name and Log fold change (LogFC). This is a optional file for GO terms and pathways, with default NULL.
expressionfile_genetype	refers to the gene type of expressionfile_significant file, which can be "REFSEQ", "ENTREZID", "SYMBOL", or other gene types that can be used in clusterProfiler, with default NULL.

Value

Outputs a dot-plot figure of enrichment.

Examples

Enrich_plot(regiongenealls_significant, enrichterm = "GOgroup", Dbannotation = "org.Mm.eg.db", title = "Biological process for significant gene")
Enrich_plot(regiongenealls_significant, enrichterm = "GO", Dbannotation = "org.Mm.eg.db", title = "Go term for significant gene")
Enrich_plot(regiongenealls_significant, enrichterm = "GO", Dbannotation = "org.Hs.eg.db", title = "Go term for significant gene") # for human data #
Enrich_plot(regiongenealls_significant, adjustpvaluecut = 0.2, enrichterm = "pathway", Dbannotation = "org.Mm.eg.db", keggorganism = "mmu", title = "Pathway for significant gene")
Enrich_plot(regiongenealls_significant, enrichterm = "pathway", keggorganism = "hsa", Dbannotation = "org.Hs.eg.db", category = FALSE, title = "Pathway for significant gene") # for human data #

expressionfile_significant <- read.table(paste(system.file(package = "GeneDMRs"), "/methdata/DEgenes.txt", sep=""), header = T) # read DEgene file #

Enrich_plot(regiongenealls_significant, adjustpvaluecut = 0.2, enrichterm = "GO", Dbannotation = "org.Mm.eg.db", title = "Go term for significant gene in two categories",
expressionfile_significant = expressionfile_significant, expressionfile_genetype = "SYMBOL")
Enrich_plot(regiongenealls_significant, enrichterm = "pathway", Dbannotation = "org.Mm.eg.db", keggorganism = "mmu", title = "Pathway for significant gene in two categories",
expressionfile_significant = expressionfile_significant, expressionfile_genetype = "SYMBOL")

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.