gdPlot {GenomeGraphs} | R Documentation

## gdPlot is the main plotting function of the GenomeGraphs package

### 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)

[Package GenomeGraphs version 1.42.0 Index]