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This script replicates a designated (master) gate hierarchy to all the samples in a group, creating linked gates. Any changes to the master are automatically updated in the linked gates.
This script replicates some—but not all—of the functionality of Cloning Gates.
Like any other script, this script can be copied, and the relevant variables changed in the copies. This copying allows you to make multiple versions of the script, each working on different master gates and/or within different groups.


  • All linked gates must be in the same group as the master.
  • Only rectangular gates are supported.


  1. Set up the gating hierarchy you want to duplicate across samples.

  2. Import the script into FlowJo:

  3. From the repository’s file Advanced_Relative_Gate.txt, copy the script text.

  4. In FlowJo, open the Script Editor (Tool tab > Cytometry band > Script Editor).

  5. In the Script Editor window, click the New Script button (marked with a plus sign) to create a new script.

  6. Paste the script text into the text pane (the middle pane).

  7. (Optional) Double-click the new script’s name (“New Script” by default), and give it a more descriptive name, such as "Relative Gate.”

  8. Define the following five fields in the script. (These fields are case-sensitive.)

* __var group_name__ This variable sets the search scope for the search.
* __var pop_path_master__ This variable sets the master gate. All changes must be made to this gate.
* __var x_param__ This variable sets the X-axis parameter.
* __var y_param__ This variable sets the Y-axis parameter.
* __var new_pop_name__ This variable sets the name that will be given to the linked gates.
  1. At the top of the Script window, click Run.

FlowJo creates linked gates in every sample in the group that contains the update/create name. The new gates are identical to the master gate. Any changes to the master gate are immediately reflected in the linked gates.