R: Class "ColorCoding"

ColorCoding-class {oompaBase} | R Documentation

## Class "ColorCoding"

### 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

`v` | a logical vector
`color` | a string or integer representing a color
`mark` | an integer representing a plotting symbol, or list of plotting symbols that should be associated with levels of the factor `fac`
`fac` | A factor
`colorScheme` | A list of colors that should be associated with levels of the factor `fac`

### 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.

### Objects from the Class

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

`v`

  a logical vector

`color`

  a string or integer representing a color

`mark`

  an integer representing a plotting symbol

### 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 krc@silicovore.com, P. Roebuck proebuck@mdanderson.org

### See Also

`ColorCodedPair`

### Examples

    showClass("ColorCoding")

    theta <- (0:360)*pi/180
    x <- cos(theta)
    y <- sin(theta)
    xp <- x > 0
    yp <- y > 0
    colors <- list(ColorCoding(xp&yp, oompaColor$BORING),
                   ColorCoding(xp&!yp, oompaColor$TOP.TEN),
                   ColorCoding(!xp&yp, oompaColor$BOTTOM.TEN),
                   ColorCoding(!xp&!yp, oompaColor$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(oompaColor$BORING, oompaColor$SIGNIFICANT,
                   oompaColor$EXPECTED, oompaColor$OBSERVED,
                   oompaColor$PERMTEST, oompaColor$FITTED,
                   oompaColor$CENTRAL.LINE, oompaColor$CONFIDENCE.CURVE,
                   oompaColor$BAD.REPLICATE, oompaColor$WORST.REPLICATE,
                   oompaColor$FOLD.DIFFERENCE, oompaColor$BAD.REPLICATE.RATIO,
                   oompaColor$TOP.TEN, oompaColor$BOTTOM.TEN,
                   oompaColor$TOP.TEN.SOLO, oompaColor$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)

[Package oompaBase version 3.2.6 Index]