FlowJo v9 Manual



Groups are the heart of all the powerful tools in FlowJo. A group is a collection of samples-and a mechanism by which analyses can be applied uniformly to that collection of samples. Any given sample may belong to one or more groups. FlowJo lists the groups in the upper portion of the workspace window.

There is a special case group: the "All Samples" group. It contains (by definition) all of the samples known to the workspace. The "All Samples" group can neither be renamed nor deleted.

Groups are created in one of two ways:

(1) When you read in a folder of data files, FlowJo creates a group with the name of the folder and automatically adds the samples to the group; or

(2) You can create a new group by clicking on the New Group button under the Workspace menu.

When you create the group, you are given the option of adding samples to the group which fit a set of criteria-this is specified by the Group Definition dialog window. In addition, you can specify that these criteria should be checked anytime new samples are added to the workspace: if the new samples meet those criteria, they are added to the group (and group-based analyses are automatically performed at once.)

You can add samples from the workspace to any group. Just click on the sample and drag it to the group. To remove a sample from a group, select the group, then select the sample and press the delete key. If the current group is All Samples and you delete the sample, then you will be permanently removing the sample from the workspace.

A group behaves in some ways as a "template sample" for its members. In other words, you can drag gates or statistic nodes to a group exactly the same way as you would to another sample. The only difference is that these gates, after being added to the group, are then added to every sample belonging to the group. This is one of the ways in which FlowJo performs batch analyses. For hints on creating groups to efficiently use this feature, click here.

There is one unbreakable rule with regards to groups: Every sample belonging to a group must contain every analysis that has been applied to the group. Of course, if the group specifies analyses that are not applicable to the sample, then this doesn't happen. (For example, if you have created a gate based on compensated parameters, and a sample that is not compensated is added to the group, then those gates cannot be added to that sample. Once you compensate the sample, however, the gates will be automatically added.)

If a sample belongs to multiple groups, then it will have all of the analyses from all of the groups to which it belongs. Whenever you add a sample to a group (by dragging it into the group), that group's analyses are automatically applied to the sample.

Associated with group names is a color and text style. A gate that is attached to a sample through a group operation appears in the same color and style as that group. Therefore, any gate within a sample that has a group's color and style is guaranteed to be identical to the group's version of that gate. When you change a group's version of a gate (by dragging a new version of that gate onto the group or if you have the Synchronize Group's Gates option checked), then all samples with the group's version of the gate are likewise updated.

If you modify a sample's version of a group's gate (for instance, if you decide that a lymphocyte gate for one sample should be slightly different and you move it), then that gate will now appear in the workspace window in black and plain text (unlike the group's gates). This is how you can tell from the text when a gate has been modified. However, if you checked the Synchronize Group's Gates option when you created the group, any time you modify a gate on any sample, the group's gate is automatically updated.

Note that modified gates will still behave in other ways like group gates: when you attach a subpopulation to a group's gate, it will be attached to the same gate in all samples, whether or not they are identical to the group's version of the gate.

If you have modified a gate and decide later that it should be identical to the group's version, you can select the gate and choose the Unify analyses option under the Workspace menu. Likewise, if you select a gate within a group and choose this menu option, then all sample's versions of this gate are made identical to the group's version.

How do you know what the group's version of a gate looks like? Simply open any sample which has the group's version of the gate (i.e. the node is displayed in the color and text style of the group). If you change this sample's gate (move it), then you are only changing that sample's version. To change the group's version, drag the node back onto the group after you have made the modification or if you checked the Synchronize Group's Gates option when creating the group, the update happens automatically.

If a sample belongs to multiple groups which all have an analysis of the same name, then the sample's version of the gate will be whichever one it got first.

Deleting nodes associated with groups have special consequences:

  • If you delete the node in the group itself, then it is removed from the group. You are then asked if you want to remove the same nodes from all of the samples; if you choose not to remove them from the samples, they are left alone (but they are then owned by the samples-i.e., drawn in black and plain text-since they no longer belong to a group).
  • You cannot delete a sample's node which is identical to the group's node, since every sample must have every analysis belonging to the groups that it is in.
  • If you delete a node which is a modified version of the group's node, then FlowJo will replace it with the original, group's version of the node.
  • If you delete a sample from a group, then it is removed from the group but all analyses which came from the group are still applied to the sample (but they are now owned by the sample, not the group).
  • If you delete a group, then all of the group's analyses nodes are assigned to the samples.
  • If you rename a sample's version of a group node, then a copy of that node is made with the new name, and the sample will retain a node with the same name as the group's node.
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