GRangesAnnotationTrack-class {igvR} | R Documentation

## Constructor for GRangesAnnotationTrack

### Description

`GRangesAnnotationTrack` creates and `IGV` track for bed-like objects expressed as GRanges

### Usage

    GRangesAnnotationTrack(
      trackName,
      annotationData,
      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.
`annotationData` | A GRanges object with optional name metadata column
`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 GRangesAnnotationTrack object

### Examples

    base.loc <- 88883100
    tbl <- data.frame(chrom=rep("chr5", 3),
                      start=c(base.loc, base.loc+100, base.loc + 250),
                      end=c(base.loc + 50, base.loc+120, base.loc+290),
                      name=c("a", "b", "c"),
                      strand=rep("*", 3),
                      stringsAsFactors=FALSE)

    gr <- GRanges(tbl)
    track <- GRangesAnnotationTrack("GRangesQTest", gr)

[Package igvR version 1.10.0 Index]