visualizeCircos-methods: Generate circos plot per cluster

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Description

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

Usage

## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric'
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

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.