HighlightRegion-class {GenomeGraphs} | R Documentation

## Class "HighlightRegion" is used to highlight vertical blocks of genomic regions.

### Description

HighlightRegion is used to highlight a genomic region of interest. The class offers the ability to highlight or block out regions of interest.

### Objects from the Class

Objects can be created by calls of the form `new("HighlightRegion", ...)`.

### Slots

`start`:

  Object of class `"numeric"` genomic start position.

`end`:

  Object of class `"numeric"` genomic end position.

`region`:

  Object of class `"numericOrNull"` start and end number of the tracks to be covered by the region. These start from the first track (top = 1) to the last track: `length(gdObjects)` in the call to `gdObject`

`coords`:

  Object of class `"character"` can be either "genomic" or "absolute", if the coordinates are "absolute" then one can plot things using the coordinate space defined by: lower-left (0,0) upper-right (1,1). In this case, start = x0, end = x1 and then region = (y0, y1). See the examples for more details.

`dp`:

  Object of class `"DisplayPars"` specifys the various display parameters.

### Extends

Class `"gdObject"`, directly.

### Methods

No methods defined with class "HighlightRegion" in the signature.

### Author(s)

James Bullard

### Examples

    if (interactive()) {
    data("exampleData", package="GenomeGraphs")

    ga <- new("GenomeAxis")
    grF <- new("GeneRegion", start = 10000, end = 20000, chromosome = "I", strand = "+", biomart = yeastMart)
    grR <- new("GeneRegion", start = 10000, end = 20000, chromosome = "I", strand = "-", biomart = yeastMart)
    bt <- new("BaseTrack", base = yeastCons1[,1], value = yeastCons1[,2])
    hr1 <- new("HighlightRegion", start = 11000, end = 13000,
               dp = DisplayPars(alpha = 1, color = "red", lty = "dashed", lwd = 3))
    hr2 <- new("HighlightRegion", start = 15900, end = 16500)

    gdPlot(list(grF, ga, grR, bt), highlightRegions = list(hr1, hr2))
    }

[Package GenomeGraphs version 1.42.0 Index]