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 right corner 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

Tucked into the top of the vertical scroll bar is a miniature tool palette, containing an arrow 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 arrow after any new object is created.

The arrow 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.  Option-drag to duplicate them.  Start a drag in the background of the layout editor, and it will draw out a rectangle.  Upon finishing the drag, the layout editor will select all objects that are enclosed by that rectangle.

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 to change the order of the layout.  Double click on the rectangle or use the Get Info command from the Layout menu 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 or use the Get Info command from the Layout menu 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.

The grid tool will create a matrix of cells within your layout. Each cell may contain text, charts, images, or other grids. The grids provides a convenient mechanism to group and align multiple elements of the layout. Grids are explained in greater detail on the feature's own page.

Inserting Pictures

You can add graphics from other sources into FlowJo layouts. If the graphic is in PICT format (a Mac standard) then insert graphics simply by pasting them from the clipboard. To include GIF, JPEG or TIFF files, use the Insert Picture... command in the Layout 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

Across the top of the layout window are four buttons, describing the standard functions of launching another program, saving to disk, copying to the clipboard and printing.  The launch helper application function will activate your favorite graphic program and transfer the data to it. To do this, FlowJo must save the data as a file, so the first thing you will see is a request for a file name and location. Once you have saved the file, FlowJo will attempt to transfer control to the application, as listed in the bottom of the Layout preferences pane. The Save operation will create a graphics file of the current layout at its current iteration value.  Depending on the setting in the Export preferences pane, this may be written as a standard Macintosh PICT file, or a GIF, TIFF or JPEG file for special purpose exports. The PICT file is the recommended format, as it contains additional grouping information that can be useful in further editing. PICT files are readable by virtually all graphics programs on the Macintosh, and most of the popular Windows editing packages.

The Copy command puts the layout onto the Clipboard, and can be transferred to your favorite graphics package.  Note that certain settings of FlowJo can cause it to make a picture where every dot in a dot plot is a separate element in the picture.  In particularly large files, this has been know to overtax other programs ability to paste the contents of the clipboard.  If you are having troubles pasting pictures copied from FlowJo, you should go to the Preferences and turn off the setting "Don't Export Bitmaps".

The Print button will cause the current version of the layout to be sent to your chosen printer.  Print settings can be controlled either by the Page Setup… command in the File menu, or by the Setup… button in the lower left corner of the window.  If you want to print the current layout from several different values or samples, you should use the Iteration controls to build a Frames Set, and print from that window.

Iteration Controls

Across the top right corner of the window, just under the Direct Output controls, 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 button containing a stack of reports is the Iterate command button.  Pressing this will take you to FlowJo's Batch Processing Dialog. It will prompt you to choose from one of four report types: making a new layout, tiled report, web page, or movie.

The rightmost control, the yellow 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. You can also use the page up and page down keys to move through the iteration.

Page Setup And Magnification

In the bottom left corner of the window are additional controls that govern the scaling of the layout, either (in the case of the Setup... button) on the printed page, or on the screen.  The "Setup…" button will bring up the Mac's standard Page Setup dialog, allowing you to set options such as the Printer defaults, the paper size, the paper orientation and the scaling.  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.  Changing the Page Setup options will generally cause the page breaks to be redrawn to reflect the new page size and scale. In addition to changing the scaling from the Page Setup... dialog, you can also place the mouse over the intersection of any of the gray pagination lines and rescale the magnification just by dragging the page size larger and smaller.

The page size can also be resized automatically using the Page Scaling popup menu or manually by dragging the corners of the page outlines in the layout editor. The Page Scaling popup will provide commands to Scale to Page Width or Scale To Page Height. These will measure the size of the layout, and then rescale so as to make the desired dimension fit. The option Scale to Page chooses between Scale to Page Width and Scale To Page Height, finding the option that leaves the images as large as possible, while still fitting them on the page.

Those settings set the way the layout is scaled to fit the printed page. The settings on the right side of the control strip govern how the layout is scaled to be displayed on the screen. The smaller buttons showing distant and closer mountains zoom in and out, that is they reduce and increase the magnification within the layout window.  The popup menu allows you to set the magnification directly.  Scales from 12.5% to 200% of the original size are available. The keyboard commands Cmd-[ and Cmd-] will also zoom in and out, respectively.

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