This page is dedicated to the control of boxplot colors, using the ggplot2 library. The first example on the left shows how to set a uniform color for the whole boxplot. Remember the transparency is set using the alpha argument. The second example set a different color to each group. To get it, simply set the color argument in the aesthetic.

We can use different color palettes. Here are 2 examples using R color brewer. Note that a continuous palette is used on the left, whereas a discrete palette is used on the right. See graph #38 for all the available palette.

If you want to highlight one or several groups:

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