% fields, Tools for spatial data
% Copyright 2004-2011, Institute for Mathematics Applied Geosciences
% University Corporation for Atmospheric Research
% Licensed under the GPL -- www.gpl.org/licenses/gpl.html

\name{tim.colors}
\alias{tim.colors}
\alias{larry.colors}
\alias{two.colors}
\alias{designer.colors}
\alias{color.scale}
\title{ Some useful color tables for images and tools to handle them. }
\description{
Several color scales useful for image plots:
a pleasing rainbow style color table patterned after that used in 
Matlab by Tim Hoar and also some  simple color interpolation schemes between
two or more colors. There is also a function that converts between colors and 
a real valued vector.
}
\usage{
tim.colors(n = 64, alpha=1.0)
larry.colors()
two.colors(n=256, start="darkgreen", end="red", middle="white", alpha=1.0)
designer.colors( n=256, col= c("darkgreen", "white", "darkred"),
                              x= seq(0,1,, length(col)) ,alpha=1.0)
color.scale( z, col=tim.colors(256), zlim =NULL, transparent.color="white",                     eps= 1e-8) 

}
\arguments{
\item{alpha}{The transparency of the color -- 1.0 is opaque and 0 is transparent.
             This is useful for overlays of color and still being able to view
              the graphics that is covered. }
  \item{n}{ Number of color levels. The setting \code{n}=64 is the orignal 
definition.}
\item{start}{Starting color for lowest values in color scale}
\item{end}{ Ending color.}
\item{middle}{Color scale passes through this color at halfway}
\item{col}{A list of colors (names or hex values) to interpolate}
\item{x}{Positions of colors on a [0,1] scale. Default is to assume that
the x values are equally spacesd from 0 to 1.}
\item{z}{Real vector to encode in a color table.}
\item{zlim}{Range to use for color scale. Default is the \code{range(z)} inflated by 
1- eps and 1+eps.}
\item{transparent.color}{Color value to use for NA's or values outside \code{zlim}}
\item{eps}{A small inflation of the range to avoid boundary values of \code{z} being 
coded as NAs}
}

\details{
 The color in R can be represented as three vectors in RGB coordinates
and these coordinates are interpolated separately using a cubic spline
to give color values that intermediate to the specified colors.  

 Ask Tim Hoar about \code{tim.colors}! He is a matlab black belt and this is
his favorite scale in that system.  \code{two.colors} is really about
three different colors. For other colors try \code{fields.color.picker}
to view possible choices.   \code{start="darkgreen", end="azure4"} are
the options used to get a nice color scale for rendering aerial photos
of ski trails.  (See \url{http://www.image.ucar.edu/Data/MJProject}.)
\code{larry.colors} is a 13 color palette used by Larry McDaniel and is particularly 
useful for visualizing  fields of climate variables.

 \code{designer.color} is the master function for two.colors and
tim.colors.  It can be useful if one wants to customize the color table
to match quantiles of a distribution.  e.g. if the median of the data is
at .3 with respect to the range then set \code{x} equal to c(0,.3,1) and
specify three colors to provide a transtion that matches the median
value. In fields language this function interpolates between a set of
colors at locations x. While you can be creative about these colors just
using another color scale as the basis is easy. For example

\code{designer.color( 256, rainbow(4), x= c( 0,.2,.8,1.0))}

leaves the choice of the colors to Dr. R after a thunderstorm.
 
}
\value{

A vector giving the colors in a hexadecimal format, two extra hex digits are added for alpha channel. 

}
\seealso{ topo.colors, terrain.colors, image.plot, quilt.plot, grey.scale,
fields.color.picker }
\examples{

tim.colors(10) 
# returns an array of 10 character strings encoding colors in hex format

# e.g. (red, green,  blue) values of   (16,255, 239)
#   translates to "#10FFEF" 
# rgb( 16/255, 255/255, 239/255, alpha=.5)
#   gives   "#10FFEF80"  note extra "alpha channel"

# veiw some color table choices
set.panel( 2,3)
z<- outer( 1:20,1:20, "+")
obj<- list( x=1:20,y=1:20,z=z )

image( obj, col=tim.colors( 200)) # 200 levels

image( obj, col=two.colors() )

# using tranparency without alpha the image plot would cover points
plot( 1:20,1:20)
image(obj, col=two.colors(alpha=.5), add=TRUE)

coltab<- designer.colors(col=c("blue", "grey", "green"),  x= c( 0,.3,1) ) 
image( obj, col= coltab )

# peg colors at some desired quantiles  of data.
# NOTE need 0 and 1 for the color scale to make sense
x<- quantile( c(z), c(0,.25,.5,.75,1.0) )
# scale these to [0,1]
zr<- range( c(z))
x<- (x-zr[1])/ (zr[2] - zr[1])  

coltab<- designer.colors(256,rainbow(5), x)
image( z, col= coltab ) # see image.plot for adding all kinds of legends

# colors now change at quantiles of data

# some random color values
set.seed(123)
z<- rnorm(100)
hex.codes<- color.scale(z, col=two.colors())
N<-length( hex.codes)
# take a look at the coded values
# or equivalently create some Xmas wrapping paper!
image( 1:N, N, matrix(1:N, N,1) , col=hex.codes, axes=FALSE, xlab="", ylab="")

set.panel()

}
\keyword{ aplot}