Colors in R can be defined by name (blue, black, darkgoldenrod, cornsilk, etc.), according to RGB values, according to HSL and HCL values (variously, permutations of [Wikipedia:hue|hue]], saturation, chroma and luminescence, see: Wikipedia:HSL and HSV and Wikipedia:Munsell color system), most definable either as decimal values between 0 to 1 or hexadecimal values between 0 and F.
See the colors command for a list of built in colros.
See rgb, hsv and hcl commands for more on defining custom colors.
See heat.colors, topo.colors and rainbow for automatic generation of appealing color spectra.
Here are a few links to handy R color charts: