multiplot {rCGH} | R Documentation

## Static Genomic Profile and LOH Visualization

### Description

This function display a static view of the genomic profile and the allelic difference stored in an object of class `"rCGH"`.
If no allelic difference is available, the genomic profile only is displayed.

### Usage

    ## S4 method for signature 'rCGH'
    multiplot(object, symbol=NULL, gain=.5,
        loss=(-.5), minLen=10, pCol = "grey50", GLcol = c("blue", "red3"),
        L=matrix(seq(1, 12)), p=c(1/2, 1/4, 1/4), Title=NULL, ylim=NULL)

### Arguments

`object` | : An object of class `"rCGH"`
`symbol` | : character. A valid HUGO symbol (case insensitive).
`gain` | : numeric. A gain threshold value (in Log2(Ratio)). Segments greater, or equal to, this value will be colored, as specified by `GLcol`.
`loss` | : numeric. A loss threshold value (in Log2(Ratio)). Segments lower, or equal to, this value will be colored, as specified by `GLcol`.
`minLen` | : numeric. The mininal length for a segment, expressed in Kb. When `NULL` (default), segments are reported as they have been computed by `segmentCGH`. Segments shorter than the specified value are re-merged otherwise.
`pCol` | : string. The probe points color. Default is `"grey50"`.
`GLcol` | : vector. A vector of 2 colors: the gained and lost segments colors, respectively. Default is `"blue"` for gains and `"red3"` for losses.
`L` | : matrix. A matrix defining the layout. Default is 12 lines.
`p` | : numeric. The proportion of each plot within the plot window. Default is `1/2, 1/4, 1/4`, which corresponds to 6-4-4 lines for the genomic profile in Log2R, in copy number, and the LOH plot, respectiviely, and given a 12-line layout.
`Title` | : character string. A title for the plot. If `NULL` (default), the sample name (when exists) is used.
`ylim` | : numeric. A vector of two values specifying the y-axis range. See `plotProfile`.

### Value

None.

### Note

If no allelic difference is available, the genomic profile only is displayed.

### Author(s)

Frederic Commo

### See Also

`plotDensity`, `plotProfile`, `plotLOH`, `view`

### Examples

    filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
        package = "rCGH")
    cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")
    cgh <- adjustSignal(cgh, nCores=1)
    cgh <- segmentCGH(cgh, nCores=1)
    cgh <- EMnormalize(cgh)

    # Static visalizations
    multiplot(cgh, symbol = "erbb2")

[Package rCGH version 1.16.0 Index]