When you have more than one object selected in the Layout Editor, you can align them relative to each other.  Choose "Align..." from the "Layout" menu (or press command-K), and FlowJo will show you the following dialog:

Here you can choose exactly how to align the objects.  Choose "Align" to make the selected edges at the same level (for example, "Align Top" means the top of every object is at exactly the same level). Choose "Distribute" to place the objects at equal distances along the specified dimension (for example "Distribute Top" means that the top of each successive object is the same distance as the next).  You can also Align by "Width" or "Height", which means that objects will be placed adjacent to each other, with no space in between objects.  Distributing by "Width" or "Height" means that an equal amount of space is placed between every object.

You can also select to align graph items by their axes.  Normally, objects are aligned by the outer-most edges of the boundaries enclosing the whole object.  For graph items, this includes the axes labels, ticks, and other information.  If you choose to align by the position of the axes, however, then FlowJo considers the boundaries for alignment to be the box enclosing the graphic itself.

This gives you an easy way to create "compressed" graphics, where each graph is right next to the previous one.  First, align the graph items (by position of axes) by "Width" (or "Height") to position them adjacent to each other.  Then, for each item after the first, choose to hide the "X" or "Y" axes (as appropriate) so that the graphs appear to share the same axis.  (Hiding axes can be accomplished by clicking on a graph and selecting "Get Info...", and setting the annotation preferences for that item.)

The bottom section of the dialog supports the alignment of your graphics to a grid, which is computed from the width of the objects themselves. The objects will be lined up into rows and columns according to their current position, and then spaced either by their centers within the grid (Distribute to Grid) or by the outside edges (Align to Grid).

Group Command

Once you have elements of your layout positioned correctly, it may be desirable to Group the elements. This converts all of the individual graphs, lines, boxes and text into a single complex item that is more reusable and meaningful in future experiments.

To create a group, either use the arrow tool to encircle multiple items with a drag, or use the arrow tool in conjunction with the shift and command keys to create a multiple selection with successful clicking. Once multiple items are selected, use the Group command in the Layout menu (Cmd-G) from the layout menu to unify the selected objects. To Ungroup, click on the group and select Ungroup from the Layout menu. (Cmd-Shift-G).