Creating graphs with 3 grouping variables using GraphPad Prism.

Prism offers built-in three-way plots in conjunction with three-way ANOVA. See this page in the user guide for details. The graph looks like the one below. 

One limitation of this graph is that it is built for a 2x2xK structured ANOVA. This means that the first factor has two levels, the second factor has two levels, and the third factor has K (more than 2) levels. If you would like to create a graph that accommodates a different structure, we have some tips below. 

Start by arranging bars (or points) into groups and putting labels over or under them. Note that you can mix "interleaved" and "grouped" bars. Start with interleaved, and double click on a bar to go to Format Bars dialog box, then go to the Order and Direction tab. Here you can choose how each data set relates to the one before it. Thus, you can have B interleaved with A. Then make C start a new group, with D interleaved with it, etc.

You can draw lines to highlight the groups of bars. If you double click on a line to bring up the format dialog, you can choose "arrowheads". Some of Prism's arrowheads are really just caps, So you can draw a line that goes up, over and down to denote a group of bars. Then put a label on top. An alternative is to create boxes around groups to denote the separation. You can also add patterns within bars to further differentiate groups.