Layout Objects

A layout is created by adding objects to a blank canvas. The objects may be rectangles, lines, text or graphs. Once you have placed objects onto the canvas, you can move them (by clicking and dragging one or more selected items), resize them (by clicking and dragging on the "handles" of a selected item), or align them to each other (by selecting "Alignment..." from the "Layout" menu). The Alignment tool is a powerful tool that even lets you put multiple graphs right next to each other (i.e., abutting axes) to create a compressed view!

Rectangles, lines and text can be added via the tool palette, found in the upper left of the layout window. Select the desired tool, and drag within the editor's view in order to create a new object. The drawing tools are explained here.

To edit the color, line weight, text styles, or other information about the object, select the object and choose Properties from the Object menu. (As a shortcut, you can also double click on the object.) This will bring up one of the Object Properties dialog boxes, which provides the user interface for editing any of the graphical characteristics of the object. The content of the dialog is dependent on the type of the object. At left is an example of the dialog that comes up when you edit the definition of a text box.

Graph Objects

To add a graph to a layout, drag the node representing the population or sample from the Workspace window and drop it into the layout. This will create a new graph object in the layout editor. As with other objects, you can use the Get Info. command (or a double click) to edit the characteristics of the graph.

This dialog is devided into three panels, Specify, Annotate and Fonts.

Specify is shown at the right. There are popup menus listing the available X and Y axis parameters, as well as others to set the graph type and the optional parameters that govern the appearance of the resulting plot.

In the case of histograms, it is also possible to choose to display the Y axis as % of max, Unit Distribution, or Manual in which mode you may enter the minimum and maximum values for the Y axis. This will enable you to prevent the axis from being recalculated for each frame in the layout, and make it easier to compare successive frames of a multi-sample layout.

More description on these items can be found in the Graph Window documentation of the Graph Specification dialog.

An additional item found in this dialog is the Controls text box. This will let you specify a graph, or layer in an overlay graph, to be a control. Control graphs remain the same while others in the layout are changed as the batch process iterates through the other samples and statistics in the current group. This provides you a way to create layouts that show multiple samples, all compared to an original or control sample.

You can request the graph to Show Ancestry, meaning that all the parent populations and gates used to define this population will be shown below the graph. Below we see the final population superimposed on each of its ancestral populations.

Histogram overlays, as distinct from other graph types, have the additional option of adding an offset that produces a 3D-like plot of the multiple histograms. This separates the lines and makes it easier to compare several curves on the same graph. Any value between 0 and 100% can be used as the Amount to offset. This puts a distance between the histograms on the Z Axis. The Angle setting rotates the origin of the baseline up and away from the viewer. Values of five to twenty give useful results, but experiment. You can also drag the corner handles on the histogram overlay to change its appearance.

The second configuration panel appears when you click Annotate. It governs the additional annotation that (optionally) accompanies a graph in a layout.

The setting Show Annotation determines whether the annotation is desired at all. If you uncheck this box, FlowJo will not generate a text box associated with this graph. Assuming that it is checked, you can optionally have the annotation include the name of the sample, the name of all the gates leading to this population (the full name or full path), as well as statistics showing the frequency.

There is a setting to Show Legend for a graph. By default legends are only created for overlay graphs, where the color is used to distinguish the different data sets. But because the legend is the means to set the color and line style of histograms and dot plots, it can be useful to override the default and show legends for single data series graphs. Conversersely, there may be times when the legend is not necessary, even with multiple data sets, or you are making your own legend. In those cases, you can tell the layout editor to suppress drawing of any graph's legend.

Other settings available in this dialog include the ability to suppress either axis. This is useful if you are producing a layout with a large number of graphs and you want to save space by compressing the graphs close together and only label the outside axes.

Graphs can be resized in the Layout Editor by sewlecting the graph then dragging any of the corners.

To navigate between a graph that appears in a layout, and the graph window where its gates are defined, there is a command Open Original Graph in the Object menu. This opens the Graph Window containing the population selected in the layout. From there it is easy to navigate up the gating hierarchy to see all of the gates that define this population. Type Ctrl-O from the keyboard to open the original graph.

The third tab in the Graph Definition dialog controls the fonts of the axis labels and gate labels. (Legend fonts are adjusted by clicking the Legend Properties button on the Annotate tab.)