CDF, or Cumulative Distribution Function plots display exactly the same information as do histograms. The difference is that the histogram values are summed as the fluorescence intensity increases; thus, the CDF begins at 0% (origin) and ends at 100% (maximum Y value).
CDF plots are extremely useful for quickly finding the fluorescence of a distribution corresponding to any given percentile (such as the median). The sample plot below shows how to find the median (50th percentile), 75th, and 90th percentiles for this data. Note, that unlike the histogram, the Y-axis is labeled in units of relative frequency. In this example, the median fluorescence of the population is about 6.0 fluorescence units. See Statistics for more information.
The plot below overlays the CDF and the histogram for the same data. Put two copies
of the graph in the Layout Editor, make one copy a histogram, the other a CDF type
graph. Make the background of one transparent by setting Opacity in the Object tab to the left, adjust/remove axis labels through Graph Definitions to your liking. Lock Content on both graphs so that the other graph does not change when overlaid. Drag the transparent copy on top of the other. In this case, transparency really only matters when copy/pasting from FlowJo to another program as an image. Inside FlowJo, it’s still treated as a graph node. Next to the plot image below, is an image of the graph window edit menu, in the event you need to export your image out of FlowJo you could use one of these options.
See also the page on histograms.