gdPlot {GenomeGraphs} | R Documentation |
gdPlot is the main plotting function of the GenomeGraphs package. A collection of objects are given as a list and these will then be plotten in the order given.
gdPlot(gdObjects, minBase = NA, maxBase = NA, highlightRegions = NULL)
gdObjects |
This is either a list of gdObjects which will
be plotted from top to bottom or a single gdObjects to be plotted.
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minBase |
minBase defines the minimum base that will be
plotted, if ommitted a minimum is determined from the objects in
gdObjects if possible.
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maxBase |
maxBase defines the maximum base that will be
plotted,if ommitted a minimum is determined from the objects in
gdObjects if possible.
|
highlightRegions |
highlightRegions defines a set of
regions to overlay as rectangles on the plot. This argument is
either a list or a single HighlightRegion object.
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Steffen Durinck and James Bullard
http://www.stat.berkeley.edu/~steffen/
data("dummyData", package="GenomeGraphs") minbase = min(probestart) maxbase = max(probestart) mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") genesplus = new("GeneRegion", start = minbase, end = maxbase, strand = "+", chromosome = "3", biomart=mart) genesmin = new("GeneRegion", start = minbase, end = maxbase, strand = "-", chromosome = "3", biomart=mart) seg <- new("Segmentation", segments = segments, segmentStart = segStart, segmentEnd = segEnd, dp = DisplayPars(color = "dodgerblue2", lwd=2,lty = "dashed")) cop <- new("GenericArray", intensity = cn, probeStart = probestart, segmentation = seg, dp = DisplayPars(size=3, color = "seagreen", type="dot")) ideog = new("Ideogram", chromosome = "3") expres = new("GenericArray", intensity = intensity, probeStart = exonProbePos, dp = DisplayPars(color="darkred", type="point")) genomeAxis = new("GenomeAxis", add53 = TRUE, add35=TRUE) gdPlot(list(ideog,expres,cop,genesplus,genomeAxis,genesmin), minBase = minbase, maxBase =maxbase)