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]