colors: Color Palette for mixOmics

In mixOmics: Omics Data Integration Project

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

n	an integer, the number of colors (≥q 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.

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.

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.)

See Also

colorRamp, palette, colors for the vector of built-in "named" colors; hsv, gray, rainbow, terrain.colors, ... to construct colors; and heat.colors, topo.colors for images.

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))
}

# -----------------------
# 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)

mixOmics documentation built on June 1, 2018, 5:06 p.m.