Layout Controls
In many ways, the Layout Editor is a like a simple page layout program. It can draw boxes and lines, type text and move the items around with a familiar interface. It has some additional aspects as well: it supports multiple pages each with its own layout defined; it has controls to apply the same layout commands to many different datafiles; and most importantly, it has the ability to reference live data in the workspace so that graphs are updated when the underlying gating hierarchy changes.
Use the layout editor to create 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 the layout graphic is generated. Graphs, gates and statistics will continue to be updated in the Layout editor until your analysis is complete. 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. The Plus sign opens a new blank layout, the Equals sign opens a copy of the current layout, the Minus sign deletes the currently visible layout.
This window has a large number of controls, which are organized in groups. Pictured here is the first group on the left with their functions...
The Arrow Tool
The Arrow Tool 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. (Marquee selection.)
The Rectangle tool
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 Object > Send Backward menu command to change the order of the layout. Double click on the rectangle, use the Properties command from the Object menu or right-click and select Properties to edit the properties of the rectangle.
The Line tool
The Line Tool is used for drawing lines and arrows. Generally, you will want lines drawn on top of other elements, so draw them last or use the Object > Bring To Front command to change the order of the layout. Double click on the line or use the Object > Properties command to edit its properties. Properties supported for lines include which end has an arrowhead, line weight, and dashing pattern.
The Grid Tool
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 Grid Tool page.
The Text Tool
The Text Tool is used for adding textual annotation to the layout. To create a text box, you select the text tool from the tool bar, 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 Text Properties box. 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 be dragged and dropped into a layout. In both of those cases, a text box is created automatically.
Zooming In and Out
The Zoom tools let you view the current layout at different sizes. They do not change the resolution of the layout image or the printout size. By reducing the Zoom factor you can view a large layout that might not otherwise fit in the monitor. Click the Plus or Minus Magnifier icons to increase or decrease the layout magnification. Click the arrow between them to select a level of magnification directly, without stepping through the intervening sizes.
Inserting Pictures
You can add graphics from other sources into FlowJo layouts. To include GIF, JPEG, PNG or TIFF files, use the Insert Picture... command in the File 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
In the upper right of the layout window are tools, for copying to the clipboard, printing, and Batch processing (Iteration.)
The Copy command puts the layout onto the Clipboard, from which it 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 and choose one of several options: New Layout, Direct to Printer, PowerPoint Data, Make Movie, Write Web Page or Make PDF. The first option, New Layout, builds a tiled report which you can then print. The second, Direct to Printer, builds a report in the style of a layout (i.e., it is fully editable) which can be printed after adjusting the page breaks. PowerPoint Data saves a copy of the Batch with each page displayed as a separate slide in PowerPoint. Objects can be ungrouped and edited. Make Movie uses each page of the batch as a frame in a QuickTime movie. More details here.
Iteration Controls
Beneath the clipboard and Print icons 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.
The largest 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, the label next to the popup is Sample #, and 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 Make Batch Report... dialog. It will prompt you to choose from one of several report types: New Layout, Direct to Printer, PowerPoint Data, Make Movie, Write Web Page or Make PDF. The first option, New Layout, builds a tiled report which you can then print. The second, Direct to Printer, builds a report in the style of a layout (i.e., it is fully editable) which can be printed after adjusting the page breaks. PowerPoint Data saves a copy of the Batch with each page displayed as a separate slide in PowerPoint. Objects can be ungrouped and edited. Make Movie uses each page of the batch as a frame in a QuickTime movie. Click Here for details on using these batching methods.
The Up and Down Arrow Buttons
will set 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.
Right-clicking on a graph brings up the menu shown here.
Copy, Paste and Duplicate perform the expected functions on the graph. Properties opens the Graph Definition dialog allowing control over every aspect of the current graph, and explained more fully on this page.
Ordering lets the user control the Z order of overlapping objects in the Layout. The Z order determines which object appears to be on top of or behind other overlapping objects. You can choose to move a selected object up or down a layer in the stacking order or to the front or back of all other overlapping objects.
Add Graph Sets presents a list of graphs of your sample's attributes that can be added to the Layout with one click, for example, all fluorescent parameter combinations in a series of bivariate graphs. All of these options are described on this page.
Make Multigraph Overlay FlowJo can display multiple subpopulations of a single sample overlayed for visual comparison. Overlayed subpopulations are distinguished by color. To learn this effective display type, click here.
Edit Gates Use this command to open gating tools within the Layout Editor. A subset of the Graph Window gating tools are available. To learn more about the Layout Editor's gate editing tools, click here.
