HighlightRegion-class {GenomeGraphs} | R Documentation |
HighlightRegion is used to highlight a genomic region of interest. The class offers the ability to highlight or block out regions of interest.
Objects can be created by calls of the form new("HighlightRegion", ...)
.
start
:"numeric"
genomic start position. end
:"numeric"
genomic end
position. region
:"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
:"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
:"DisplayPars"
specifys the
various display parameters.
Class "gdObject"
, directly.
No methods defined with class "HighlightRegion" in the signature.
James Bullard
if (interactive()) { data("dummyData", 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)) }