The user can define the analysis by uploading a Flow Jo workspace. If the workspace contains a single group, then the gating template from the group will be used to define the gates. If the workspace contains more than one group, the user will choose which group to use. If the workspace contains no groups, the user will need to indicate the FCS file containing the intended gating template.

LabKey Server only understands some of the types of gates that can appear in a FlowJo workspace: polygon, rectangle, interval, and some Boolean gates (only those Boolean gates that involve subsets with the same parent). There are checkboxes for specifying which statistics (Frequency of Parent, Count, etc.) to calculate for each of the populations. Graphs are added to the analysis script for each gate in the gating template. Boolean gates do not appear in the gating template, except as statistics.

Upload FlowJo Workspace

To define an analysis as part of a script, you will upload a FlowJo workspace.

• From the Flow Scripts web part, click labkey-demo to reopen the script page.
• Click Upload FlowJo workspace under Define Analysis.

• Choose the same 'labkey-flow-demo-123/labkey-demo/Workspaces/labkey-demo.xml' workspace file you uploaded previously.
• Select which statistics you would like to be calculated. Those already defined in the FlowJo workspace are preselected.

• Click Submit.

Select the source of gating for the analysis

There is more than one group analysis in this workspace. Please specify the one to use:

• Under "Which group do you want to use?", select the labkey-demo-samples group and click Submit.

You will once again see the script main page. Now that both the compensation and the analysis have been defined, you have a full set of options for using it to analyze your data.

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