spectralMap: Draw a Spectral Map

Description Usage Arguments Value Note Author(s) References See Also Examples

Description

Generic function to draw a spectral map.

Usage

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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

spectralMap-methods, plot.mpm

Examples

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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 April 29, 2020, 5:17 a.m.

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