enrichmentPlot: plot enrichment results

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

plot enrichment results

Description

Plot the GO/KEGG/reactome enrichment results

Usage

enrichmentPlot(
  res,
  n = 20,
  strlength = Inf,
  style = c("v", "h"),
  label_wrap = 40,
  label_substring_to_remove = NULL,
  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.
style	plot vertically or horizontally
label_wrap	soft wrap the labels (i.e. descriptions of the GO or PATHWAY terms), default to 40 characters.
label_substring_to_remove	remove common substring from label, default to NULL. Special characters must be escaped. E.g. if you would like to remove "Homo sapiens (human)" from labels, you must use "Homo sapiens \\( human\\)".
orderBy	order the data by pvalue, termId or none.

Value

an object of ggplot

Author(s)

Jianhong Ou, Kai Hu

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$gr1)
     enrichmentPlot(over$gr2, style = "h")
 }

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.