Clone Gates

Please note: this functionality requires FlowJo for Mac 9.3b5 or later.

Introduction

The use case for this feature came from our clinically inclined users who wanted one version of a gate propagated to different points in a hierarchy. This used to be done by one of two ways, neither of which is optimal in terms of workflow:

• Create a version of the gate at a top level, and at each point in the tree, insert a boolean gate that refers solely to that top gate

• Create the gate; copies of the gate are FJML where each vertex refers to the vertex of the original gate

We implemented a new gate type, a "clone". Once you create a gate, you can choose to "clone" it, and apply it to different points in the sample hierarchy. Both the original and all copies are then designated as a "clones". Whenever a clone is modified, all of its clones are also modified (including renaming it). Thus, a clone can be modified at any point in the tree, and all of its versions will update appropriately.

Detailed Description 

• Any gate can be defined as a "clone". This is just a property of a gate. A clone can be unique in a sample, or there may be multiple clones of the gate in different places in the hierarchy. All clones in a sample will be identical; modify any one of them and all update. To clone a gate, select it, and choose Workspace->Clone Gate. It can be un-cloned via the same menu operation.

• A clone gate is designated by a special additional icon in front of the gate name (3 identical green circles) :
  
  

• There can be no other gates with the same name as a "clone" gate in the sample. If you specify that "CD4" is a clone (in the /Lymphs/CD3 gate), then you can't have any other gate named "CD4" anywhere else in the hierarchy. Once you've defined "CD4" as a clone, you can drag it to other places and clone it. (Alternatively, if you specify that "CD4" is a clone and there are other "CD4" gates, the program could allow you to force them to all become clones, I think that's reasonable).

• Note: If you drag a clone (e.g. "CD4") into a destination sample, then ALL "CD4" gates in that destination sample will automatically become clones.

Brief Example 

Let's link and display quad gates on all levels of a T cell analysis to show effect of different gates on contents of quads.

First, take a regular analysis with quads attached only in the relevant spot:

Select the quads and “clone” them from the Workspace menu:

Next, copy the clones to other points in the hierarchy:

And finally display them in the layout:

Now adjusting the quads in any graph window that displays this set, will update it for all 4 plots.

Comments

[Katarina Antonsdotter]

Absolutely fabulous site, with Flow Jo and FACS analysis! I have been forced to work with this method and am still confused...

I wonder if you could help me with a simple question? I have recently aquired my data on an Eclipse, advancing from Calibur, and I am afraid that I put the settings wrong in the acquisition because when I open the samples in Flow Jo I have a condensed, small collection of cells. I would like to try to change the axis range to perhaps see my T cell population better...
Do you know how to do this in Flow Jo 7.5?

Thanks a lot for your help, and for sharing your input!
Kind regards,
Katarina

PhD student
Dept Rheumatology and Inflammation Research
Gothenburg University

[maciej simm]

Hello Katarina,

the settings you're after (Ranges of parameters) are found in the T button which should be adjacent to your X and Y axes in hte graph window.

From the T button you can transform Lin log, as well as en/dis/able biexponential transforms.

For FCS3 data (I cant remember if eclipse writes that, or FCS2..), you can also use the T button to set custom start/end point of a scale. So on a cyometer with a 17M range, if you only want to see a small portion of that, you can use the "adjust parameter range" function to do just that.

Anything you do in T button SHOULD propagate to equivalent parameters in all your samples, but just to be sure, there is a "T-> apply settings to all.." macro as well.

cheers,

Maciej

[Katarina Antonsdotter]

Hi Maciej,
sorry missed your reply here. Just wanted to say thank you so much, I managed to do this. =)

Cheers,
Katarina