igvAnnotationTrack-class {igvR} | R Documentation

## Constructor for igvAnnotationTrack

### Description

Constructor for igvAnnotationTrack

### Usage

    igvAnnotationTrack(trackName, annotation, fileFormat = c("bed"),
      color = "gray", displayMode = c("SQUISHED", "COLLAPSED", "EXPANDED"),
      sourceType = "file", trackHeight = 30, 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` | An opague type, currently either a data.frame, GRanges, or UCSCBed object from rtracklayer.
`fileFormat` | Only "bed" is currently supported.
`color` | A CSS color name (e.g., "red" or "#FF0000")
`displayMode` | "COLLAPSED", "EXPANDED", or "SQUISHED"
`sourceType` | Only "file" sources are currently supported.
`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.

### Value

An igvAnnotationTrack object

[Package igvR version 1.6.1 Index]