Description Usage Arguments Details Value Slots Methods Author(s) See Also Examples

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

1 2 3 | ```
ColorCodedPair(x, y, ccl)
## S4 method for signature 'ColorCodedPair,missing'
plot(x, y, ...)
``` |

`x` |
numeric vector (for |

`y` |
numeric vector |

`ccl` |
list of |

`...` |
additional arguments are as in the underlying generic methods. |

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.

The constructor returns a valid `ColorCodedPair`

object.

The `plot`

method invisibly returns the object being plotted.

`x`

numeric vector

`y`

numeric vector

`colorCodingList`

list of

`ColorCoding`

objects

- plot(object, ...)
Plot the

`ColorCodedPair`

object, with appropriate colors and symbols (of course).

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
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')
``` |

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