Changing the color of an item is prohibited on Shabbos. Food, however, is not included in this prohibition according to most authorities. Therefore, if for example one would like to change the appearance of a white cup of wine and make it red by adding some grape juice, this would be permitted.
However, if the item that one is coloring is not something one plans on eating it is forbidden to do so. For example, a toilet bowl flush cleaner that colors the water should not be used on Shabbos. One may place the cleaner in the tank as this will cause the coloring but not do so directly.