mixOmics2: Omics Data Integration Project

################################################################################
# Authors:
#   Ignacio Gonzalez, Genopole Toulouse Midi-Pyrenees, France
#
# created: 2015
# last modified:
#
# Copyright (C) 2015
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
################################################################################


#-- jet colors --#
#----------------#






#' Color Palette for mixOmics
#'
#' The functions create a vector of \code{n} "contiguous" colors (except the
#' \code{color.mixo} which are colors used internally to fit our logo colors).
#'
#' The function \code{color.jet(n)} create color scheme, beginning with dark
#' blue, ranging through shades of blue, cyan, green, yellow and red, and
#' ending with dark red. This colors palette is suitable for displaying ordered
#' (symmetric) data, with \code{n} giving the number of colors desired.
#'
#' @aliases color.jet color.spectral color.GreenRed color.mixo
#' @param n an integer, the number of colors \eqn{(\geq 1)} to be in the
#' palette.
#' @param alpha a numeric value between 0 and 1 for alpha channel (opacity).
#' @param num.vector for \code{color.mixo} an integer vector specifying which
#' colors to use in the mixOmics palette (there are only 10 colors available.
#' @return For \code{color.jet(n)}, \code{color.spectral(n)},
#' \code{color.GreenRed(n)} a character vector, \code{cv}, of color names. This
#' can be used either to create a user-defined color palette for subsequent
#' graphics by \code{palette(cv)}, a \code{col=} specification in graphics
#' functions or in \code{par}.
#'
#' For \code{color.mixo}, a vector of colors matching the mixOmics logo (10
#' colors max.)
#' @seealso \code{\link{colorRamp}}, \code{\link{palette}},
#' \code{\link{colors}} for the vector of built-in "named" colors;
#' \code{\link{hsv}}, \code{\link{gray}}, \code{\link{rainbow}},
#' \code{\link{terrain.colors}}, ... to construct colors; and
#' \code{\link{heat.colors}}, \code{\link{topo.colors}} for images.
#' @keywords color
#' @examples
#'
#' # -----------------------
#' # jet colors
#' # ----------------------
#' par(mfrow = c(3, 1))
#' z <- seq(-1, 1, length = 125)
#' for (n in c(11, 33, 125)) {
#' image(matrix(z, ncol = 1), col = color.jet(n),
#' xaxt = 'n', yaxt = 'n', main = paste('n = ', n))
#' box()
#' par(usr = c(-1, 1, -1, 1))
#' axis(1, at = c(-1, 0, 1))
#' }
#'
#' \dontrun{
#' # -----------------------
#' # spectral colors
#' # ----------------------
#' par(mfrow = c(3, 1))
#' z <- seq(-1, 1, length = 125)
#' for (n in c(11, 33, 125)) {
#' image(matrix(z, ncol = 1), col = color.spectral(n),
#' xaxt = 'n', yaxt = 'n', main = paste('n = ', n))
#' box()
#' par(usr = c(-1, 1, -1, 1))
#' axis(1, at = c(-1, 0, 1))
#' }
#'
#' # -----------------------
#' # GreenRed colors
#' # ----------------------
#' par(mfrow = c(3, 1))
#' z <- seq(-1, 1, length = 125)
#' for (n in c(11, 33, 125)) {
#' image(matrix(z, ncol = 1), col = color.GreenRed(n),
#' xaxt = 'n', yaxt = 'n', main = paste('n = ', n))
#' box()
#' par(usr = c(-1, 1, -1, 1))
#' axis(1, at = c(-1, 0, 1))
#' }
#'
#' # # --------------------------------
#' # mixOmics colors
#' # # -------------------------------
#' X <- nutrimouse$lipid
#' Y <- nutrimouse$gene
#' nutri.res <- rcc(X, Y, ncomp = 3, lambda1 = 0.064, lambda2 = 0.008)
#'
#' my.colors = color.mixo(1:5)
#' my.pch = ifelse(nutrimouse$genotype == 'wt', 16, 17)
#' #plotIndiv(nutri.res, ind.names = FALSE, group = my.colors, pch = my.pch, cex = 1.5)
#' }
#'
#' @importFrom grDevices colorRamp
#' @export color.jet
color.jet =
function (n, alpha = 1)
{
    #-- checking general input parameters -------------------------------------#
    #--------------------------------------------------------------------------#

    #-- n
    if (length(n) > 1 || !is.finite(n))
    stop("'n' must be an integer positive value.", call. = FALSE)

    if (n < 1)
    stop("'n' must be an integer positive value.", call. = FALSE)

    #-- alpha
    if (length(alpha) > 1 || !is.finite(alpha))
    stop("'alpha' must be an numeric value in the range [0, 1].", call. = FALSE)

    if (alpha < 0 || alpha > 1)
    stop("'alpha' must be an numeric value in the range [0, 1].", call. = FALSE)

    alpha = round(255 * alpha)

    #-- end checking --#
    #------------------#

    ramp = colorRamp(c("#00008F", "#00009F", "#0000AF", "#0000BF", "#0000CF",
    "#0000DF", "#0000EF", "#0000FF", "#0010FF", "#0020FF",
    "#0030FF", "#0040FF", "#0050FF", "#0060FF", "#0070FF",
    "#0080FF", "#008FFF", "#009FFF", "#00AFFF", "#00BFFF",
    "#00CFFF", "#00DFFF", "#00EFFF", "#00FFFF", "#10FFEF",
    "#20FFDF", "#30FFCF", "#40FFBF", "#50FFAF", "#60FF9F",
    "#70FF8F", "#80FF80", "#8FFF70", "#9FFF60", "#AFFF50",
    "#BFFF40", "#CFFF30", "#DFFF20", "#EFFF10", "#FFFF00",
    "#FFEF00", "#FFDF00", "#FFCF00", "#FFBF00", "#FFAF00",
    "#FF9F00", "#FF8F00", "#FF8000", "#FF7000", "#FF6000",
    "#FF5000", "#FF4000", "#FF3000", "#FF2000", "#FF1000",
    "#FF0000", "#EF0000", "#DF0000", "#CF0000", "#BF0000",
    "#AF0000", "#9F0000", "#8F0000", "#800000"),
    space = "Lab")

    rgb(ramp(seq(0, 1, length = n)), alpha = alpha, maxColorValue = 255)
}