In addition to regular overlay options, FlowJo can display multiple parameter overlay combinations for visual comparison. Overlayed subpopulations are distinguished by color - the color of a subset allows easy assessment of its characteristics on multiple plots.

To begin, drag a sample from the Workspace into the Layout Editor. Then drag any other subpopulations or populations from other samples on top of the existing plot to create the initial overlay.

Next, right-click the overlayed plots and select Make MultiGraph Overlay from the menu.
Then choose from the sub-menu available options :

Show All Histograms this option will show the overlay of the populations as histograms.

Show All By ___ this option will show the overlay of the populations against whatever parameter is showing on the Y-axis. This option displays as bivariate overlays.

Show NxN this option will display both univariate and bivariate plots as a matrix of overlays.
(This feature limits the number of visible dimensions to the first six fluorochromes, if more exist.)