TwoChannelMicroarrayColor: Class representing two-channel microarray colors

In HenrikBengtsson/R.colors: Color and color filter classes

Description

Class representing two-channel microarray colors.

Usage

TwoChannelMicroarrayColor(ch1=NULL, ch2=NULL, maxColorValue=65535, log2Cutoff=5, hueRange=c(HsvgColor$RED.HUE, HsvgColor$GREEN.HUE), hueIntensityColor="hsvg")

Arguments

ch1,ch2	numeric vectors reprensenting the signals in each channel. The signals should be in the range [0,maxColorValue].
maxColorValue	numeric specifying the maximum signal value.
log2Cutoff	numeric specifying the cutoff level of the absolute log-ratios (base 2). Absolute log-ratios above this level will be made equal to log2Cutoff.
hueRange	A vector of two integers or a character string, specifying the hue (color) range that the log-ratios should span.
hueIntensityColor	A function or a Color class that takes the arguments hue and intensity, or a character string specifying which color class. This specifies the class of colors from which the microarray colors should be generated.

Details

TO DO: "In the fluorescent double-staining micrographs, DNA chips, etc, do not use the combination of red and green. Use magenta (purple) and green instead." [1].

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

References

[1] Masataka Okabe and Kei Ito, Barrier-free presentation that is friendly to colorblind, http://jfly.iam.u-tokyo.ac.jp/html/color_blind/#stain

Examples

layout(matrix(1:4, ncol=2, byrow=TRUE))

TwoChannelMicroarrayColor$demo()

if ("dichromat" %in% library()$results) {
  ofilter <- Color$setColorFilter(DichromatColorFilter())
  TwoChannelMicroarrayColor$demo()
 
  Color$setColorFilter(DichromatColorFilter(type="protan"))
  TwoChannelMicroarrayColor$demo()
}

Color$setColorFilter(GrayColorFilter())
TwoChannelMicroarrayColor$demo()

if ("dichromat" %in% library()$results) {
  Color$setColorFilter(ofilter)
}

HenrikBengtsson/R.colors documentation built on May 6, 2019, 11:53 p.m.