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.
colormap( z = NULL, zlim, zclip = FALSE, breaks, col = oceColorsJet, name, x0, x1, col0, col1, blend = 0, missingColor, debug = getOption("oceDebug") )
z  an optional vector or other set of numerical values to be examined.
If 

zlim  optional vector containing two numbers that specify the 
zclip  logical, with 
breaks  an optional indication of break points between color levels
(see 
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

name  an optional string naming a builtin colormap (one of

x0, x1, col0, col1  Vectors that specify a color map. They must all be
the same length, with 
blend  a number indicating how to blend colors within each band.
This is ignored except when 
missingColor  color to use for missing values. If not provided, this
will be 
debug  a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more. 
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 twoelement 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 samenamed 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 samenamed 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.
This is a multipurpose 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 predefined 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 valuecolor 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.
Information on GMT software is given at
http://gmt.soest.hawaii.edu
(link worked for years but failed
20151212). 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 20151208), and numerical specifications for some
color maps are at http://www.beamreach.org/maps/gmt/share/cpt,
http://soliton.vm.bytemark.co.uk/pub/cptcity, and other sources.
Other things related to colors:
oceColors9B()
,
oceColorsCDOM()
,
oceColorsChlorophyll()
,
oceColorsClosure()
,
oceColorsDensity()
,
oceColorsFreesurface()
,
oceColorsGebco()
,
oceColorsJet()
,
oceColorsOxygen()
,
oceColorsPAR()
,
oceColorsPalette()
,
oceColorsPhase()
,
oceColorsSalinity()
,
oceColorsTemperature()
,
oceColorsTurbidity()
,
oceColorsTurbo()
,
oceColorsTwo()
,
oceColorsVelocity()
,
oceColorsViridis()
,
oceColorsVorticity()
,
ocecolors
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) if (FALSE) { ## 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$col) ## Example 4. image of world topography with water colorized ## smoothly from violet at 8km depth to blue ## at 4km depth, then blending in 0.5km increments ## to white at the coast, with tan for land. cm < colormap(x0=c(8000, 4000, 0, 100), x1=c(4000, 0, 100, 5000), col0=c("violet","blue","white","tan"), col1=c("blue","white","tan","yellow")) lon < topoWorld[['longitude']] lat < topoWorld[['latitude']] z < topoWorld[['z']] imagep(lon, lat, z, breaks=cm$breaks, col=cm$col) contour(lon, lat, z, levels=0, add=TRUE) ## Example 5. visualize GMT style color map cm < colormap(name="gmt_globe", debug=4) plot(seq_along(cm$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) }