spectralMap: Generic function to draw a spectral map, according to JnJ...

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Generic function to draw a spectral map, according to JnJ Standards

Usage

spectralMap(object, groups, ...)

Arguments

object	object of class ExpressionSet
groups	string indicating the name of the column in the phenoData that defines the groups
...	further arguments to be passed to the methods

Value

Object of class plot.mpm, i.e. the S3 output object of the plot.mpm function of the mpm package

Note

Coloring of groups on the spectralMap uses the a4 palette as produced by a4palette

Author(s)

Tobias Verbeke

References

Wouters, L., Goehlmann, H., Bijnens, L., Kass, S.U., Molenberghs, G., Lewi, P.J. (2003). Graphical exploration of gene expression data: a comparative study of three multivariate methods. Biometrics 59, 1131-1140. Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman \& Hall/CRC, pp. 148 - 153.

See Also

plot.mpm

Examples

if (require(ALL)){
	data(ALL, package = "ALL")
	ALL <- addGeneInfo(ALL)
	spectralMap(object = ALL, groups = "BT", legendPos = 'bottomright')
	spectralMap(object = ALL, groups = "BT",
	 plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
					dim = c(1,2), sampleNames = FALSE, zoom = c(1,5), col.size = 2, 
					do.smoothScatter = TRUE))
	spectralMap(object = ALL, groups = "BT",
			plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65,
					dim = c(1,2), sampleNames = as.character(pData(ALL)$BT),
					zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE))
}

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.