HighlightRegion-class: Class "HighlightRegion" is used to highlight vertical blocks...

In GenomeGraphs: Plotting genomic information from Ensembl

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))
}

Example output

Loading required package: biomaRt
Loading required package: grid

GenomeGraphs documentation built on Oct. 31, 2019, 4:34 a.m.