plotTopLOLAEnrichments {LOLA} | R Documentation |
Given some results (you grab the top ones on your own), this plots a barplot visualizing their odds ratios.
plotTopLOLAEnrichments(data)
data |
A results table returned from runLOLA() |
Returns a ggplot2 plot object.
dbPath = system.file("extdata", "hg19", package="LOLA") regionDB = loadRegionDB(dbLocation=dbPath) data("sample_universe", package="LOLA") data("sample_input", package="LOLA") getRegionSet(regionDB, collections="ucsc_example", filenames="vistaEnhancers.bed") getRegionSet(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed") getRegionFile(dbPath, collections="ucsc_example", filenames="vistaEnhancers.bed") res = runLOLA(userSets, userUniverse, regionDB, cores=1) locResult = res[2,] extractEnrichmentOverlaps(locResult, userSets, regionDB) writeCombinedEnrichment(locResult, "temp_outfolder") userSetsRedefined = redefineUserSets(userSets, userUniverse) resRedefined = runLOLA(userSetsRedefined, userUniverse, regionDB, cores=1) g = plotTopLOLAEnrichments(resRedefined)