Use the layout editor to define a new layout definition. A layout definition is not the output data itself.  Instead it is the specification of which graphs will be placed at what locations, when it is generated.  You can have as many layout definitions in the workspace as you wish.  You can create new empty definitions or delete them using the buttons in the top left corner of the window.

This window has a large number of controls, which are organized in groups.  Below is an enlargement of the top of the layout window, showing the groups of buttons in the window. Clicking on any of the buttons in the graphic below will scroll you to the section of this page that describes that group of controls.

Tool Palette

At the top left of the Layout Editor is a tool palette, containing an selection cursor tool, a rectangle tool, a line tool, and a text tool.  Only one tool is active at a time, and the active tool will return to the selection cursor after any new object is created.

The cursor is used to select existing objects. Click on an object to select it (as shown by dark handles at the corners of the object).  Use the shift key to select additional items.  Drag items to move them.  Start a drag in the background of the layout editor, and it will select all objects that are enclosed by the drag.

The rectangle tool is used for drawing simple boxes and frames.  If you create the rectangle surrounding another element, and want it to serve as a background, use the Send To Back command (under the Edit menu) to change the order of the layout.  Double click on the rectangle to edit the properties of the rectangle.

The line tool is used for drawing lines and arrows.  Generally, you will want lines drawn on top of move other elements, so draw them last or use the Bring To Front command to change the order of the layout.  Double click on the line to edit its properties. Properties supported for lines include which side has an arrowhead, line weight, and dashing pattern.

The text tool is used for adding textual annotation to the layout.  To create a text box, you select the text tool from the tools, and click once or drag out a rectangle in the layout view.  When you create a new text box, a dialog will appear to help you edit the text.  This is called the FJML Editor. FlowJo uses a custom markup language, not unlike the HTML used in web pages, to richly express the structure of your flow analysis. Once you confirm changes via the mouse or the Enter key, or click the mouse on a different object in the layout, the editing stops, and the layout editor text is reformatted and frozen. To edit it again, double click on the text box to return it to the edit state.  Text clippings or statistics from the workspace can dragged and dropped into a layout.  In both of those cases, a text box is created automatically.

Inserting Pictures

You can add graphics from other sources into FlowJo layouts. Use the Insert Picture... command in the Object menu. This is a way to include institution or laboratory logos or backgrounds from other sources into your FlowJo layouts. Like boxes and arrows, the pictures are replicated in each frame of an iteration.

Direct Output Commands

At the top right of the layout window are three buttons, describing the standard functions of copying to the clipboard, saving to disk, and printing.  The Save operation will create a graphics file of the current layout at its current iteration value.  Depending on the setting in the preferences, this may be written as a JPEG, SVG, GIF, TIFF or EPS file.

The Copy command puts the layout onto the Clipboard, and can be transferred to your favorite graphics package. 

The Print button will cause the current version of the layout to be sent to your chosen printer.  If you want to print the current layout from several different values or samples, you should use the Batch button to build a layout from all the samples and print from that window.

Iteration Controls

Across the top right corner of the window, is a row of controls used to change the sample or samples currently viewed in layout.  It is easy to take a layout viewing one of your samples and its associated gates and statistics, and see the same displays applied to other data.  Use of the iteration controls is discussed in context in Example 2.

The largest and leftmost control is a pop-up menu containing all values of the current attribute that exist in the current group.  If the current attribute is sample identifier, then all of the samples in the current group will be listed in the menu.  If another keyword has been set to be the iteration attribute via the Iteration Options dialog, then all values of that attribute will be listed.  In a patient study, this may be a Patient ID, a date or therapy for which multiple samples have been drawn and collected.

The Batch button is the Iterate command button.  Pressing this will take you to FlowJo's Batch Processing Dialog to create a new layout by gathering the graphs, stats, lines, boxes and text boxes from all the samples in the group. The rightmost control, the up and down buttons, will reset the iteration attribute to its next or previous value.  This is convenient for quickly looking through multiple layouts, without generating the entire set of them.

Page Setup And Magnification

At the top of the layout editor window are additional controls that govern the scaling of the layout on the screen. The - button zooms out and the + button zooms in. The popup menu allows you to set the magnification directly.  Scales from 12% to 400% of the original size are available.

You will notice that the layout editor draws light gray lines signifying where the page breaks would be if you were to print the layout.  You can place the mouse over the intersection of any of the gray pagination lines and rescale the magnification by dragging the page size larger and smaller. This setting is the way the layout is scaled to fit the printed page.

The Use Placeholders button is discussed later in its own page.