visualizeInteractions {R3CPET} | R Documentation |
This method can be used to draw a circos plot of the chromatin interactions located in the given genomic range.
## S4 method for signature 'ChiapetExperimentData,GRanges' visualizeInteractions(object, range)
object |
a |
range |
a |
A ciros plot of the selected region is displayed and a list containing the following objects is returned.
circos
:a GRanges
object that contains the involved chromatin interactions.
plot
:a ggplot
object containing plot.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
ChiapetExperimentData
, loadPETs
, ggbio
, GRanges
petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt") tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz") ## Not run: x <- ChiapetExperimentData(pet = petFile, tfbs= tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) ## plot intractions in the region of interest gr <- GRanges("chr1", IRanges(1240000,10300000)) p <- visualizeInteractions(x, gr) p ## End(Not run)