enrichmentPlot {ChIPpeakAnno}R Documentation

plot enrichment results

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)
 }

[Package ChIPpeakAnno version 3.28.0 Index]