The ColorCoding class

Description

A class for associating plotting symbols and colors with a logical vector or with levels of a factor.

Usage

ColorCoding(v, color, mark = 1)
colorCode(fac, colorScheme = 1:length(levels(fac)), mark = 1)

Arguments

Details

It is often necessary with microarray data to produce multiple plots, where each point on the plot corresponds to a gene or a spot on the microarray. Across multiple plots, we often want to use symbols or colors to mark subsets of he genes with certain properties. The ColorCoding class works in tandem with the ColorCodedPair class to make it easier to maintain consistent plotting conventions across multiple graphs.

Value

The constructor returns a valid object of the ColorCoding class.
The colorCode function provides a simple interface to associate colors and symbols with the levels of a factor. It returns a list of valid ColorCoding objects that can be passed directly to the constructor of a ColorCodedPair object.

Creating Objects

Although objects can be created using new, the preferred method is to use the constructor function, ColorCoding. To create a set of colors and symbols associated with different levels of a factor, use the colorCode function.

Slots

Methods

There are no specialized methods for objects of this class; all activities can be performed by directly accessing the documented slots.

Author(s)

Kevin R. Coombes <kcoombes@mdanderson.org>

See Also

The ColorCodedPair class

Examples

theta <- (0:360)*pi/180
x <- cos(theta)
y <- sin(theta)
xp <- x > 0
yp <- y > 0
colors <- list(ColorCoding(xp&yp, COLOR.BORING),
               ColorCoding(xp&!yp, COLOR.TOP.TEN),
               ColorCoding(!xp&yp, COLOR.BOTTOM.TEN),
               ColorCoding(!xp&!yp, COLOR.CONFIDENCE.CURVE))
plot(ColorCodedPair(x, y, colors))

plot(ColorCodedPair(theta, x, colors))

plot(ColorCodedPair(theta, y, colors),
     xlab='angle in radians', ylab='sine', main='colored sine')

fac <- factor(rep(c('left', 'right'), c(180, 181)))
colors <- colorCode(fac, c('blue', 'red'))
plot(ColorCodedPair(x, y, colors))

# cleanup
rm(x, y, xp, yp, theta, colors, fac)

colorList <- c(COLOR.BORING, COLOR.SIGNIFICANT,
               COLOR.EXPECTED, COLOR.OBSERVED,
               COLOR.PERMTEST, COLOR.FITTED,
               COLOR.CENTRAL.LINE, COLOR.CONFIDENCE.CURVE,
               COLOR.BAD.REPLICATE, COLOR.WORST.REPLICATE,
               COLOR.FOLD.DIFFERENCE, COLOR.BAD.REPLICATE.RATIO,
               COLOR.TOP.TEN, COLOR.BOTTOM.TEN,
               COLOR.TOP.TEN.SOLO, COLOR.BOTTOM.TEN.SOLO
               )
plot(c(1,4), c(1,4), type='n')
for (i in 1:4) {
  for (j in 1:4) {
    points(i,j, col=colorList[i + 4*(j-1)], pch=16, cex=4)
  }
}
rm(colorList, i, j)