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, overlays = NULL, labelColor = "black", labelCex = 1, labelRot = 90)
gdObjects |
This is either a list of gdObjects which will
be plotted from top to bottom or a single gdObjects to be plotted.
|
minBase |
minBase defines the minimum base that will be
plotted, if ommitted a minimum is determined from the objects in
gdObjects if possible.
|
maxBase |
maxBase defines the maximum base that will be
plotted,if ommitted a minimum is determined from the objects in
gdObjects if possible.
|
overlays |
overlays defines a set of
regions to overlay on the plot. This argument is
either a list or a single Overlay object.
|
labelColor |
Draw the labels with the given colors. |
labelCex |
Character expansion factor. |
labelRot |
Rotate the track labels labelRot degrees. |
Steffen Durinck and James Bullard
http://www.stat.berkeley.edu/~steffen/
data("exampleData", 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)