gdPlot: gdPlot is the main plotting function of the GenomeGraphs...

In GenomeGraphs: Plotting genomic information from Ensembl

Description

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.

Usage

gdPlot(gdObjects, minBase = NA, maxBase = NA, overlays = NULL,
              labelColor = "black", labelCex = 1, labelRot = 90)

Arguments

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.

Author(s)

Steffen Durinck and James Bullard

References

http://www.stat.berkeley.edu/~steffen/

Examples

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[[1]], 
           segmentStart = segStart[[1]], segmentEnd = segEnd[[1]],
           dp = DisplayPars(color = "dodgerblue2", lwd=2,lty = "dashed"))

cop <- new("GenericArray", intensity  = cn, probeStart = probestart, 
           trackOverlay =  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)

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