a4 (version 1.20.0)

spectralMap: Draw a Spectral Map

Description

Generic function to draw a spectral map.

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

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

spectralMap-methods, 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))
}