marray: maDefaultPar – R documentation

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maDefaultPar

Default graphical parameters for microarray objects

Description

This function returns default graphical parameters for microarray objects. The parameters may be passed as arguments to the functions maBoxplot and maPlot.

Usage

maDefaultPar(m, x, y, z)

Arguments

`m`	Microarray object of class `"marrayRaw"` and `"marrayNorm"`.
`x`	Name of accessor method for the abscissa spot statistic, typically a slot name for the microarray object `m`, such as `maA`.
`y`	Name of accessor method for the ordinate spot statistic, typically a slot name for the microarray object `m`, such as `maM`.
`z`	Name of accessor method for the spot statistic used to stratify the data, typically a slot name for the microarray layout object (see `"marrayLayout"`) such as `maPlate` or a method such as `maPrintTip`.

Value

A list with elements

`def.box`	default graphical parameters for `maBoxplot`.
`def.plot`	default graphical parameters for `maPlot`.
`def.lines`	default graphical parameters for functions such as `maLoessLines` used in `maPlot`.
`def.legend`	default graphical parameters for functions such as `maLegendLines` used in `maPlot`.
`def.text`	default graphical parameters for functions such as `maText` used in `maPlot`.

Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.

References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.

Examples

# See examples for maPlot.

marray

Exploratory analysis for two-color spotted microarray data

v1.68.0

LGPL

Authors

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.

Initial release

2009-08-15