multiplot: Static Genomic Profile and LOH Visualization

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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")

rCGH documentation built on Nov. 8, 2020, 8:30 p.m.