oce (version 1.0-1)

colormap: Calculate color map

Description

Map values to colors, for use in palettes and plots. There are many ways to use this function, and some study of the arguments should prove fruitful in cases that extend far beyond the examples.

Usage

colormap(z = NULL, zlim, zclip = FALSE, breaks, col = oceColorsJet,
  name, x0, x1, col0, col1, blend = 0, missingColor,
  debug = getOption("oceDebug"))

Arguments

z

an optional vector or other set of numerical values to be examined. If z is given, the return value will contain an item named zcol that will be a vector of the same length as z, containing a color for each point. If z is not given, zcol will contain just one item, the color "black".

zlim

optional vector containing two numbers that specify the z limits for the color scale. If provided, it overrides defaults as describe in the following. If name is given, then the range of numerical values contained therein will be used for zlim. Otherwise, if z is given, then its rangeExtended sets zlim. Otherwise, if x0 and x1 are given, then their range sets zlim. Otherwise, there is no way to infer zlim and indeed there is no way to construct a colormap, so an error is reported. It is an error to specify both zlim and breaks, if the length of the latter does not equal 1.

zclip

logical, with TRUE indicating that z values outside the range of zlim or breaks should be painted with missingColor and FALSE indicating that these values should be painted with the nearest in-range color.

breaks

an optional indication of break points between color levels (see image). If this is provided, the arguments name through blend are all ignored (see “Details”). If it is provided, then it may either be a vector of break points, or a single number indicating the desired number of break points to be computed with pretty(z, breaks). In either case of non-missing breaks, the resultant break points must number 1 plus the number of colors (see col).

col

either a vector of colors or a function taking a numerical value as its single argument and returning a vector of colors. The value of col is ignored if name is provided, or if x0 through col1 are provided.

name

an optional string naming a built-in colormap (one of "gmt_relief", "gmt_ocean", "gmt_globe" or "gmt_gebco") or the name of a file or URL that contains a color map specification in GMT format, e.g. one of the .cpt files from http://www.beamreach.org/maps/gmt/share/cpt). If name is provided, then x0, x1, col0 and col1 are all ignored.

x0, x1, col0, col1

Vectors that specify a color map. They must all be the same length, with x0 and x1 being numerical values, and col0 and col1 being colors. The colors may be strings (e.g. "red") or colors as defined by rgb or hsv.

blend

a number indicating how to blend colors within each band. This is ignored except when x0 through col1 are supplied. A value of 0 means to use col0[i] through the interval x0[i] to x1[i]. A value of 1 means to use col1[i] in that interval. A value between 0 and 1 means to blend between the two colors according to the stated fraction. Values exceeding 1 are an error at present, but there is a plan to use this to indicate subintervals, so a smooth palette can be created from a few colors.

missingColor

color to use for missing values. If not provided, this will be "gray", unless name is given, in which case it comes from that color table.

debug

a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.

Value

A list containing the following (not necessarily in this order)

• zcol, a vector of colors for z, if z was provided, otherwise "black"

• zlim, a two-element vector suitable as the argument of the same name supplied to image or imagep

• breaks and col, vectors of breakpoints and colors, suitable as the same-named arguments to image or imagep

• zclip the provided value of zclip.

• x0 and x1, numerical vectors of the sides of color intervals, and col0 and col1, vectors of corresponding colors. The meaning is the same as on input. The purpose of returning these four vectors is to permit users to alter color mapping, as in example 3 in “Examples”.

• missingColor, a color that could be used to specify missing values, e.g. as the same-named argument to imagep. If this is supplied as an argument, its value is repeated in the return value. Otherwise, its value is either "gray" or, in the case of name being given, the value in the GMT color map specification.

• colfunction, a univariate function that returns a vector of colors, given a vector of z values; see Example 6.

Details

This is a multi-purpose function that generally links (``maps'') numerical values to colors. The return value can specify colors for points on a graph, or breaks and col vectors that are suitable for use by drawPalette, imagep or image.

There are three ways of specifying color schemes, and colormap works by checking for each condition in turn.

• Case A. Supply z but nothing else. In this case, breaks will be set to pretty(z, 10) and things are otherwise as in case B.

• Case B. Supply breaks. In this case, breaks and col are used together to specify a color scheme. If col is a function, then it is expected to take a single numerical argument that specifies the number of colors, and this number will be set to length(breaks)-1. Otherwise, col may be a vector of colors, and its length must be one less than the number of breaks. (NB. if breaks is given, then all other arguments except col and missingColor are ignored.) The figure below explains the (breaks, col) method of specifying a color mapping. Note that there must be one more break than color. This is the method used by e.g. image.

• Case C. Do not supply breaks, but supply name instead. This name may be the name of a pre-defined color palette ("gmt_relief", "gmt_ocean", "gmt_globe" or "gmt_gebco"), or it may be the name of a file (including a URL) containing a color map in the GMT format (see “References”). (NB. if name is given, then all other arguments except z and missingColor are ignored.)

• Case D. Do not supply either breaks or name, but instead supply each of x0, x1, col0, and col1. These values are specify a value-color mapping that is similar to that used for GMT color maps. The method works by using seq to interpolate between the elements of the x0 vector. The same is done for x1. Similarly, colorRampPalette is used to interpolate between the colors in the col0 vector, and the same is done for col1. The figure above explains the (x0, x1, col0, col1) method of specifying a color mapping. Note that the each of the items has the same length. The case of blend=0, which has color col0[i] between x0[i] and x1[i], is illustrated below.

References

Information on GMT software is given at http://gmt.soest.hawaii.edu (link worked for years but failed 2015-12-12). Diagrams showing the GMT color schemes are at http://www.geos.ed.ac.uk/it/howto/GMT/CPT/palettes.html (link worked for years but failed 2015-12-08), and numerical specifications for some color maps are at http://www.beamreach.org/maps/gmt/share/cpt, http://soliton.vm.bytemark.co.uk/pub/cpt-city, and other sources.

See Also

Other things related to colors: oceColors9B, oceColorsCDOM, oceColorsChlorophyll, oceColorsClosure, oceColorsDensity, oceColorsFreesurface, oceColorsGebco, oceColorsJet, oceColorsOxygen, oceColorsPAR, oceColorsPalette, oceColorsPhase, oceColorsSalinity, oceColorsTemperature, oceColorsTurbidity, oceColorsTwo, oceColorsVelocity, oceColorsViridis, oceColorsVorticity, ocecolors

Examples

# NOT RUN {
library(oce)
## Example 1. color scheme for points on xy plot
x <- seq(0, 1, length.out=40)
y <- sin(2 * pi * x)
par(mar=c(3, 3, 1, 1))
mar <- par('mar') # prevent margin creep by drawPalette()
## First, default breaks
c <- colormap(y)
drawPalette(c$zlim, col=c$col, breaks=c$breaks)
plot(x, y, bg=c$zcol, pch=21, cex=1)
grid()
par(mar=mar)
## Second, 100 breaks, yielding a smoother palette
c <- colormap(y, breaks=100)
drawPalette(c$zlim, col=c$col, breaks=c$breaks)
plot(x, y, bg=c$zcol, pch=21, cex=1)
grid()
par(mar=mar)

# }
# NOT RUN {
## Example 2. topographic image with a standard color scheme
par(mfrow=c(1,1))
data(topoWorld)
cm <- colormap(name="gmt_globe")
imagep(topoWorld, breaks=cm$breaks, col=cm$col)

## Example 3. topographic image with modified colors,
## black for depths below 4km.
cm <- colormap(name="gmt_globe")
deep <- cm$x0 < -4000
cm$col0[deep] <- 'black'
cm$col1[deep] <- 'black'
cm <- colormap(x0=cm$x0, x1=cm$x1, col0=cm$col0, col1=cm$col1)
imagep(topoWorld, breaks=cm$breaks, col=cm$col)

## Example 4. image of world topography with water colorized
## smoothly from violet at 8km depth to blue
## at 4km depth, then blending in 0.5km increments
## to white at the coast, with tan for land.
cm <- colormap(x0=c(-8000, -4000,   0,  100),
               x1=c(-4000,     0, 100, 5000),
               col0=c("violet","blue","white","tan"),
               col1=c("blue","white","tan","yelloe"),
               blend=c(100, 8, 0))
lon <- topoWorld[['longitude']]
lat <- topoWorld[['latitude']]
z <- topoWorld[['z']]
imagep(lon, lat, z, breaks=cm$breaks, col=cm$col)
contour(lon, lat, z, levels=0, add=TRUE)
message("colormap() example 4 is broken")

## Example 5. visualize GMT style color map
cm <- colormap(name="gmt_globe", debug=4)
plot(seq_along(cm$x0), cm$x0, pch=21, bg=cm$col0)
grid()
points(seq_along(cm$x1), cm$x1, pch=21, bg=cm$col1)

## Example 6. colfunction
cm <- colormap(c(0, 1))
x <- 1:10
y <- (x - 5.5)^2
z <- seq(0, 1, length.out=length(x))
drawPalette(colormap=cm)
plot(x, y, pch=21, bg=cm$colfunction(z), cex=3)
# }