Groups in FlowJo™

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Hello, Tim with FlowJo here. In this video, I'm going to discuss how to create and edit groups, make groups dynamic so that you can automatically parse samples out into your various groups without you dragging and dropping the samples between them. Groups are found within this groups pane in the work space. It's the middle section of the workspace window. Groups act like file folders to parse out your samples into manageable units so that you can perform a unique function on a sub set of samples within the work space. For example, I have this group called "Master Gates" in this work space, where I've applied a uniform master gating approach so that all the blue gates get applied to any sample within this master gates group. I know that all of the blue gates that are group owned by my master gates group are identical between the different samples within that group. So every blue gate is the same.

I can also generate unique reports on sub sets and samples by clicking on the FMOs group here. It isolates just the 14 control samples, and maybe I want to generate a report from my layout editor only on the FMO samples. I can do that, by selecting in my iteration options the FMOs group, and then when I generate a batch report it will only show the samples within that group in my report output.

Group creation is done with a button here called the create group action button. It's located up in the static toolbar. It's got a command g hot key to initiate. Then the action button is also located within the navigate band of actions under the FlowJo tab here. If I create a group I am prompted with this create group user interface where I have to give my group a name, give it a color, that will be the color that it shows here in the naming of that group in the groups pane. I can give it a text style formatting for that name, an option role. Groups start out as what we call live groups. That means that if you set any inclusion criteria for samples, either a panel of reagents that these samples were stained for, or some keyword information like the $FIL keyword, that's the file name of the sample.

You can use features in the sample to parse out the samples into the correct groups without you dragging and dropping them. The groups become dynamic when they're live and samples go into those groups based on the sample inclusion criteria that you set up in this window right here. Let's go ahead and make a group. Maybe I want to isolate my 20 experimental all stained samples. If I make a group and give it that name, "20 Experimental All Stained Samples", I can give it a color, let's make it a nice pink color. Give it a text style, bold italic sounds good to me, and a role. This is going to be a real test group because these are my experiments, but you can give your group a role of controls as I've done with my FMOs group over here. A test group role, a gating level role, or a compensation group role. Really the roles are up to you, how you want to specify them, unless you want to perform compensation on a set of samples, then you need to label the group as a compensation group to allow the matrix calculation to occur.

I'm going to call this one a test group, because it is a real experiment, and the group is already live when I start it. I don't have any other panels, except for this one in this experiment, so I'm not going to use the panel stain reagents to parse samples out but instead I'm going to use, from this drop down menu for keywords, I can use the file name, the file URI, any other user entered keyword information. That is meta data assigned to those samples so you can sort them out, or push out things like patient IDs, or other information that you label these samples with. In this case I'm going to use the $FIL keyword, that's the filename as I've mentioned. I'm going to say, from this next drop down list, if the $FIL contains the acronym LD, for lab donor, these are my lab donor samples, and I want those LD samples to go into this 20 experimental all stained group.

When I create the group I get the group over here, created, along with it says the role of tests. It's got the color and style formatting that I specified, and it contains 20 samples which all contain LD in the naming scheme. What if I want to create a group that is just my controls? I'm going to call this next group "My 14th FMO Control Samples Group." I'm going to give it a role, instead of being a test, I'm going to say this is a control group and give it a color, maybe I want to make it green, and give it italicized formatting, whatever you want to do there. I don't want to use the same inclusion criteria, because these are my all stain samples in the real experiment, instead I want to get all the FMO controls in there. Instead of saying the $FIL filename contains LD, I'm going to change this to be if $FIL contains FMO. When I create this group I get a group of 14 FMO control samples, which all have FMO in the naming scheme here.

You can actually merge and layer these choices. Up to four different keywords can be layered together, you can make them and, or, and not, so you can make the samples that are included in this group satisfy multiple criteria. Have it either/or, have it exclude samples based on their naming scheme or keyword identifiers. So let's try this with two layers. I'm going to say if the filename contains FMO or to merge it can be this or my next criteria if the filename contains LD. This type of merger, with all of my samples that are controls and my real experiment, I would probably put into something like my master gates group. If I call my 34 master gates samples that I want to go in here, give it a color, and press create group, then I get this new group with 34 samples in it, all of which have either FMO or LD in the naming scheme.

Groups, again, act like units within FlowJo to allow you to perform unique functions. If I want to merge a set of samples in a group I can select on the group and go to export concatenate. I can concatenate the group of samples together in one file if I would like to. If I want to generate a report on that group from the table editor I can set that group in my iterations options and initiate the report generated on just the samples within that group when I create my table. If I want to do a unique layout report, just on my control samples, I can set group specified in the iteration options as the FMOs group and great create a batch report to whatever file type I want. That will go through the group of samples here and generate a unique report for each of the samples in the group together.

If you have any questions about groups we have an online web docs, it's docs.flowjo.com. I would be happy to answer any questions that you have. Thanks for sticking with me through this little video on group creation. This is Tim with FlowJo, good day.