R3CPET (version 1.4.2)

visualizeCircos-methods: Generate circos plot per cluster

Description

This method generates a basic circos plot of the chromatin interaction in a given cluster.

Usage

"visualizeCircos"(object, data, cluster = 1, chrLenghts = NULL)

Arguments

object

a ChromMaintainers object in which the clusters are already calculated.

data

a ChiapetExperimentData containing the interaction data.

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.

Value

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

See Also

NetworkCollection, ChromMaintainers

Examples

    ## 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)