Select the Layout Annotation button in the Preferences tool to open the Layout Annotation preferences.



  1. Use Annotations This setting enables/disables annotations in layouts.
  2. Show Graph Title: In the graph annotation, show the title of the graph.
  3. Show Sample Name: In the graph annotation, show the sample name.
  4. Show Frequency: In the graph annotation, show the event frequency (within the whole sample).
  5. Show Population Name: In the graph annotation, show the name of the subset.
  6. Show Count: In the graph annotation, show the event count.
  7. Show Full Path: Include names of the parent gates up to the sample (the full path).

Legend Palette

  1. Select 12 colors for use in overlays: FlowJo assigns a color to each layer of an overlay. Using these color selection boxes you can set which colors will appear in what order as more plots are added.

Adjunct Histograms

  1. Adjunct Histograms: Check this box to add histograms opposite the corresponding axes of bivariate plots.
  2. Color: Select level of tinting for histogram.
  3. Style: Select line style of histogram.
  4. Weight: Select line weight of histogram.


  1. Show Legend: Check this box to include a legend beside each plot showing samplename, gating path, keywords, and other configurable content.
  2. Show Ancestry: Check this box to add plots of the parent populations beside a plot in the Layout Editor.
  3. Show Backgating: Check this box to show backgating within the ancestry plots. Backgating displays the child population in color within each parent population. Includes all parent gates up to sample, with an overlay to show gate effect.