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Each layout is a member of layout set (com.liferay.portal.model.LayoutSet). A layout set represents a group of layout pages, and thus a layout set can be thought of as a "web site", or more specifically, a "portal instance." Since each user has a private group associated with them, this allows each individual user to maintain their own custom portal.
The theme and color scheme used by a layout can either be set individually for the layout, or it is inherited from its layout set.