enrichmentPlot: plot enrichment results

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Plot the GO/KEGG/reactome enrichment results

Usage

enrichmentPlot(
  res,
  n = 20,
  strlength = 30,
  orderBy = c("pvalue", "termId", "none")
)

Arguments

res	output of getEnrichedGO, getEnrichedPATH.
n	number of terms to be plot.
strlength	shorten the description of term by the number of char.
orderBy	order the data by pvalue, termId or none.

Value

an object of ggplot

Examples

data(enrichedGO)
enrichmentPlot(enrichedGO)
if (interactive()||Sys.getenv("USER")=="jianhongou") {
     
     library(org.Hs.eg.db)
     library(GO.db)
     bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
     gr1 <- toGRanges(bed, format="BED", header=FALSE) 
     gff <- system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno")
     gr2 <- toGRanges(gff, format="GFF", header=FALSE, skip=3)
     library(EnsDb.Hsapiens.v75) ##(hg19)
     annoData <- toGRanges(EnsDb.Hsapiens.v75)
     gr1.anno <- annoPeaks(gr1, annoData)
     gr2.anno <- annoPeaks(gr2, annoData)
     over <- lapply(GRangesList(gr1=gr1.anno, gr2=gr2.anno), 
                    getEnrichedGO, orgAnn="org.Hs.eg.db",
                    maxP=.05, minGOterm=10, condense=TRUE)
     enrichmentPlot(over)
 }

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.