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Last data update: 2014.03.03

R: Microarray color palette

maPalette

R Documentation

Microarray color palette

Description

This function returns a vector of color names corresponding to a range of colors specified in the arguments.

Usage

maPalette(low = "white", high = c("green", "red"), mid=NULL, k =50)

Arguments

`low`	Color for the lower end of the color palette, specified using any of the three kinds of R colors, i.e., either a color name (an element of `colors`), a hexadecimal string of the form `"#rrggbb"`, or an integer `i` meaning `palette()[i]`.
`high`	Color for the upper end of the color palette, specified using any of the three kinds of R colors, i.e., either a color name (an element of `colors`), a hexadecimal string of the form `"#rrggbb"`, or an integer `i` meaning `palette()[i]`.
`mid`	Color for the middle portion of the color palette, specified using any of the three kinds of R colors, i.e., either a color name (an element of `colors`), a hexadecimal string of the form `"#rrggbb"`, or an integer `i` meaning `palette()[i]`.
`k`	Number of colors in the palette.

Value

A "character" vector of color names. This can be used to create a user-defined color palette for subsequent graphics by palette, in a col= specification in graphics functions, or in 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(1,4))
pal <- maPalette(low="red", high="green")
maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
pal <- maPalette(low="red", high="green", mid="yellow")
maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
pal <- maPalette()
maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
pal <- maPalette(low="purple", high="purple",mid="white")
maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(marray)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/marray/maPalette.Rd_%03d_medium.png", width=480, height=480)
> ### Name: maPalette
> ### Title: Microarray color palette
> ### Aliases: maPalette
> ### Keywords: color
> 
> ### ** Examples
> 
> par(mfrow=c(1,4))
> pal <- maPalette(low="red", high="green")
> maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
> pal <- maPalette(low="red", high="green", mid="yellow")
> maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
> pal <- maPalette()
> maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
> pal <- maPalette(low="purple", high="purple",mid="white")
> maColorBar(seq(-2,2, 0.2), col=pal, horizontal=FALSE, k=21)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>