visualizeCircos-methods {R3CPET} | R Documentation |
This method generates a basic circos plot of the chromatin interaction in a given cluster.
## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric' visualizeCircos(object, data, cluster = 1, chrLenghts = NULL)
object |
a |
data |
a |
cluster |
the number of the cluster to display |
chrLenghts |
the chromatin lengths. if not provided the package suppose it is a human chromatin and uses the corresponding lengths. Change it if you are using another species. |
circos
a GRanges
object that contains the coordinate of the left side interactions.
The right side interactions can be accessed by writing circos\$to.gr
.
plot
a ggplot
object
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
NetworkCollection
, ChromMaintainers
## get the different datasets path 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: data(RPKMS) x <- ChiapetExperimentData(pet = petFile, tfbs= tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) ## build the different indexes x <- createIndexes(x) ## build networks connecting each interacting regions nets<- buildNetworks(x) ## infer the networks hlda<- InferNetworks(nets) hlda<- clusterInteractions(hlda) visualizeCircos(hlda,x, cluster=3) ## End(Not run)