marray: maColorBar – R documentation

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maColorBar

Calibration bar for color images

Description

This function produces a color image (color bar) which can be used for the legend to another color image obtained from the functions image, maImage, or maImage.func.

Usage

maColorBar(x, horizontal=TRUE, col=heat.colors(50), scale=1:length(x), k=10, ...)

Arguments

`x`	If "numeric", a vector containing the "z" values in the color image, i.e., the values which are represented in the color image. Otherwise, a "character" vector representing colors.
`horizontal`	If `TRUE`, the values of `x` are represented as vertical color strips in the image, else, the values are represented as horizontal color strips.
`col`	Vector of colors such as that generated by `rainbow`, `heat.colors`, `topo.colors`, `terrain.colors`, or similar functions. In addition to these color palette functions, a new function `maPalette` was defined to generate color palettes from user supplied low, middle, and high color values.
`scale`	A "numeric" vector specifying the "z" values in the color image. This is used when the argument `x` is a "character" vector representing color information.
`k`	Object of class "numeric", for the number of labels displayed on the bar.
`...`	Optional graphical parameters, see `par`.

Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine, Yee Hwa (Jean) Yang.

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

par(mfrow=c(3,1))
Rcol <- maPalette(low="white", high="red", k=10)
Gcol <- maPalette(low="white", high="green", k=50)
RGcol <- maPalette(low="green", high="red", k=100)
maColorBar(Rcol)
maColorBar(Gcol, scale=c(-5,5))
maColorBar(1:50, col=RGcol)

par(mfrow=c(1,3))
x<-seq(-1, 1, by=0.01)
maColorBar(x, col=Gcol, horizontal=FALSE, k=11)
maColorBar(x, col=Gcol, horizontal=FALSE, k=21)
maColorBar(x, col=Gcol, horizontal=FALSE, k=51)

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