color.jet: Color Palette for mixOmics

Description

The functions create a vector of n "contiguous" colors (except the color.mixo which are colors used internally to fit our logo colors).

Usage

color.jet(n, alpha = 1)
color.spectral(n, alpha = 1)
color.GreenRed(n, alpha = 1)
color.mixo(num.vector)

Arguments

an integer, the number of colors $(\geq 1)$ to be in the palette.

alpha

a numeric value between 0 and 1 for alpha channel (opacity).

num.vector

for color.mixo an integer vector specifying which colors to use in the mixOmics palette (there are only 10 colors available.

Value

For color.jet(n), color.spectral(n), color.GreenRed(n) a character vector, cv, of color names. This can be used either to create a user-defined color palette for subsequent graphics by palette(cv), a col= specification in graphics functions or in par.

For color.mixo, a vector of colors matching the mixOmics logo (10 colors max.)

Details

The function 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 n giving the number of colors desired.

Examples

Run this code

# NOT RUN {
# -----------------------
# 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))
}

# -----------------------
# 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
# # -------------------------------
data(nutrimouse)
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)

# }

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