enrichmentPlot {ChIPpeakAnno} | R Documentation |
Plot the GO/KEGG/reactome enrichment results
enrichmentPlot( res, n = 20, strlength = 30, orderBy = c("pvalue", "termId", "none") )
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. |
an object of ggplot
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) }