visualizeCircos-methods {R3CPET}R Documentation

Generate circos plot per cluster

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 (nde12@mails.tsinghua.edu.cn)

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)
[Package R3CPET version 1.20.0 Index]