visualizeInteractions {R3CPET} | R Documentation

## Display a Circos plot of ChIA-pet interactions

### Description

This method can be used to draw a circos plot of the chromatin interactions located in the given genomic range.

### Usage

    ## S4 method for signature 'ChiapetExperimentData,GRanges'
    visualizeInteractions(object, range)

### Arguments

`object` | a `ChiapetExperimentData` in which the interactions are already loaded. Check `loadPETs` for more info.
`range` | a `GRanges` object containing the genomic region of interest.

### Value

A ciros plot of the selected region is displayed and a list containing the following objects is returned.

`circos` :

  a `GRanges` object that contains the involved chromatin interactions.

`plot` :

  a `ggplot` object containing plot.

### Author(s)

Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)

### See Also

`ChiapetExperimentData`, `loadPETs`, `ggbio`, `GRanges`

### Examples

      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:
      x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE)
      ## plot intractions in the region of interest
      gr <- GRanges("chr1", IRanges(1240000,10300000))
      p <- visualizeInteractions(x, gr)
      p

    ## End(Not run)

[Package R3CPET version 1.20.0 Index]