R: Class "ColorCodedPair"

ColorCodedPair-class {oompaBase} | R Documentation

## Class "ColorCodedPair"

### Description

This class represents a vector of (x,y) pairs, each of which should be plotted in a specific color with a specific symbol.

### Usage

    ColorCodedPair(x, y, ccl)
    ## S4 method for signature 'ColorCodedPair,missing'
    plot(x, y, ...)

### Arguments

`x` | numeric vector (for `ColorCodedPair`) or an object of class `ColorCodedPair` (for `plot`)
`y` | numeric vector
`ccl` | list of `ColorCoding` objects
`...` | additional arguments are as in the underlying generic methods.

### 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 `ColorCodedPair` class works in tandem with the `ColorCoding` class to make it easier to maintain consistent plotting conventions across multiple graphs.

### Value

The constructor returns a valid `ColorCodedPair` object.

The `plot` method invisibly returns the object being plotted.

### Slots

`x`

  numeric vector

`y`

  numeric vector

`colorCodingList`

  list of `ColorCoding` objects

### Methods

plot(object, ...)

  Plot the `ColorCodedPair` object, with appropriate colors and symbols (of course).

### Author(s)

Kevin R. Coombes krc@silicovore.com, P. Roebuck proebuck@mdanderson.org

### See Also

`colorCode`, `ColorCoding`

### Examples

    showClass("ColorCodedPair")

    theta <- (0:360)*pi/180
    x <- cos(theta)
    y <- sin(theta)
    xp <- x > 0
    yp <- y > 0
    colors <- list(ColorCoding(xp&yp, oompaColor$EXPECTED),
                   ColorCoding(xp&!yp, oompaColor$OBSERVED),
                   ColorCoding(!xp&yp, oompaColor$PERMTEST),
                   ColorCoding(!xp&!yp, oompaColor$FITTED))
    plot(ColorCodedPair(x, y, colors))

    plot(ColorCodedPair(theta, x, colors))

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

[Package oompaBase version 3.2.6 Index]