trackClusters {CAGEfightR} | R Documentation

## Create genome browser track of clusters.

### Description

Create a Gviz-track of clusters (unidirectional TCs or bidirectional enhancers), where cluster strand and peak is indicated.

### Usage

    trackClusters(object, ...)

    ## S4 method for signature 'GRanges'
    trackClusters(
      object,
      plusColor = "cornflowerblue",
      minusColor = "tomato",
      unstrandedColor = "hotpink",
      ...
    )

    ## S4 method for signature 'RangedSummarizedExperiment'
    trackClusters(object, ...)

### Arguments

`object` | GRanges: GRanges with peaks in the thick-column.
`...` | additional arguments passed on to GeneRegionTrack.
`plusColor` | character: Color for plus-strand features.
`minusColor` | character: Color for minus-strand features.
`unstrandedColor` | character: Color for unstranded features.

### Value

GeneRegionTrack-object.

### See Also

Other Genome Browser functions: `trackBalance()`, `trackCTSS()`, `trackLinks()`

### Examples

    library(Gviz)
    data(exampleUnidirectional)

    # Find some wide unidirectional clusters:
    TCs <- subset(exampleUnidirectional, width >= 100)

    # Create track
    clusters_track <- trackClusters(TCs[1:2,], name='Tag clusters', col=NULL)

    # Plot
    plotTracks(clusters_track)

    # See vignette for examples on how to combine multiple Gviz tracks

[Package CAGEfightR version 1.14.0 Index]