Tables

A requirement of many experiments is the ability to generate tabular output for further analysis in a spreadsheet or statistics program. The Table Editor is the means by which you can generate a series of statistical calculations for all samples in a group. These statistics can be any of the statistics FlowJo calculates: medians, frequencies, etc. You can also use this tool to generate functions that will display their output for every sample in a group as a column in the table. The Table Editor will use the column specification to iterate through all the populations in the current Workspace group. The rows of the finished table will be the populations, the columns will display their values.

From the Workspace window, open the Table Editor. This can be done in one of two ways: either click on the table editor function button in the workspace window, or select the Table Editor from the Windows menu. (Ctrl-T)

Use the Table Editor to create a new table definition. A table definition is not the output data itself.  Instead it is the specification of what columns the table will contain, when it is generated. 

You can create new empty definitions, duplicate existing ones, or delete them using the buttons in the top left corner of the window. Each different table definition listed in the left hand column of the Table Editor is a template for a table.

Dragging a population node into the Table Editor will add its frequency statistic to the table. Each statistic in the right panel of the table editor will correspond to a column in the output table; you can change the order of these columns by clicking and dragging the statistics around. You can rename a column at any time by clicking in the Custom Name column and typing the new name. The table is created for those samples in the currently-selected group: check to make sure that the appropriate group is selected in the Workspace window before you create the table!

You can add statistics and keywords to a table definition, simply by clicking on them in the Workspace window and dragging them to the definition pane on the right hand side of the Table Editor window. You can select multiple nodes in the Workspace and drag them all at once. More generally, you can click on the Column Definition button to add Statistics, Keywords and Formulas to your table whether or not you have previously defined them in the Workspace.

The Table Editor will automatically calculate these column values for each sample in the currently selected group. When you create a table, each column value in the Table Editor is applied to every applicable sample in the current group--irrespective of any population you actually dragged into the table.

When you create a table, FlowJo will cycle through all of the samples in the currently selected group. For each statistic, keyword or formula in the table definition, it searches for an appropriate population in each sample. If one is not found, then it leaves a blank for that entry. (For instance, if the statistic you created was the median FITC fluorescence of a Lymphocyte gate, and the Lymphocyte gate does not exist in all samples, then those samples will have blank values for this statistic). Therefore, the statistics are only gathered for those samples which have the appropriate stains, gates and keywords already applied to them.

Whether you define columns by dragging from the Workspace or selecting the Column Definition button, you can customize the result in the Column Information dialog. To edit the details of an existing column definition, click on the Column Info button.Here you can name the column, define it as a control value, hide it from the finished table and format the output according to criteria of your choice. If the values generated exceed an amount you choose, or have standard deviations greater or less than a chosen value, they can be formatted differently in the output table for easy recognition.

Follow these links to see how to enter and customize Statistics, Keywords and Formulas in FlowJo.

When your column definitions are complete, select the Table Generation button to view the output table. You will see the following dialog...

In the Sample data from: pull-down menu, you can choose the group that the table is about. All the groups you have defined in the Workspace will be listed here.

In the Iteration source: pull-down menu choose whether to batch through the data by sample or by keyword. The keyword list is compiled from the properties of the files in the Workspace.

Next you can choose what items will show in your finished table. Check those items you want to show. If Show Borders is checked, you can drag the slider below it to determine the thickness of the lines in your table. The black square is a button. Click on it to choose the color of the lines.

Finally, the Destination: drop-down list tells FlowJo what you want to do with the table.

• Display in FlowJo will open the table in its own window.
• Save File offers you the choice of formats shown on the right as well as a choice of directories and filename.
• Upload to FTP lets you specify the information you need to send your table to the remote storage site of your choice:

• Print brings up the familiar Windows print requester.

When you have chosen the destination of your table, select the Generate Table button to view your table.