UCSCBedAnnotationTrack-class {igvR} | R Documentation

## Constructor for UCSCBedAnnotationTrack

### Description

`UCSCBedAnnotationTrack` creates and `IGV` track for bed objects imported using `rtracklayer`

### Usage

    UCSCBedAnnotationTrack(
      trackName,
      annotation,
      color = "darkGrey",
      displayMode = "SQUISHED",
      trackHeight = 50,
      expandedRowHeight = 30,
      squishedRowHeight = 15,
      maxRows = 500,
      searchable = FALSE,
      visibilityWindow = 1e+05
    )

### Arguments

`trackName` | A character string, used as track label by igv, we recommend unique names per track.
`annotation` | A UCSCData object imported by `rtracklayer`
`color` | A CSS color name (e.g., "red" or "#FF0000")
`displayMode` | "COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
`trackHeight` | track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
`expandedRowHeight` | Height of each row of features in "EXPANDED" mode.
`squishedRowHeight` | Height of each row of features in "SQUISHED" mode, for compact viewing.
`maxRows` | of features to display
`searchable` | If TRUE, labels on annotation elements may be used in search
`visibilityWindow` | Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

### Details

Detailed description goes here

### Value

A UCSCBedAnnotationTrack object

### Examples

    bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed")
    gr.bed <- rtracklayer::import(bed.filepath)
    track <- UCSCBedAnnotationTrack("UCSC bed", gr.bed,  color="blue", displayMode="SQUISHED")

[Package igvR version 1.10.0 Index]