semantic colors {oompaBase}

Pre-defined colors for microarray plots

Description

A collection of predefined color names to help ensure consistency in multiple graphical displays of microarray data.

oompaColor:

a list containing named components allowing the user to systematically use colors for different interpretations.

oompaColor$BORING:

Used to mark uninteresting points in a plot; gray.

oompaColor$SIGNIFICANT:

Used to mark points that are statistically significant; red

oompaColor$EXPECTED:

Used to draw curves representing an expected distribution; blue

oompaColor$OBSERVED:

Used to draw curves indicating the observed distribution; darkgreen

oompaColor$PERMTEST:

Used to draw curves indicating distributions derived from a permutation test; magenta

oompaColor$FITTED:

Used to draw curves obtained by some fitting procedure, such as loess; orange

oompaColor$CENTRAL.LINE:

Used to draw lines through the centers of distributions or expected values; blue

oompaColor$CONFIDENCE.CURVE:

Used to draw confidence bounds around curves; red3

oompaColor$BAD.REPLICATE:

Used to indicate highly variable points; purple1

oompaColor$WORST.REPLICATE:

Used to mark extraordinarily variable points; purple3

oompaColor$FOLD.DIFFERENCE:

Used to indicate points with large fold difference; skyblue

oompaColor$BAD.REPLICATE.RATIO:

Used to flag points for which the ratios at replicate spots are highly variable; violetred

oompaColor$TOP.TEN:

Used to mark points in the "top ten" list; cadetblue

oompaColor$BOTTOM.TEN:

Used to mark points in "bottom ten" list of most underexpressed genes; pink

oompaColor$BOTTOM.TEN.SOLO:

Use unknown; palegreen

oompaColor$TOP.TEN.SOLO:

Use unknown; deeppink

Examples

oompaColor
x <- seq(0, 2*pi, by=0.1)
plot(x, sin(x), col=oompaColor$BORING)