| 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 above the vertical scrollbar on the right edge
of the layout window. Select the desired tool, and drag within
the editor's view in order to create a new object. [More
on Layout Tools] 
To edit the color, line weight, text styles, or
other information about the object, select the object and choose
"Get Info…" from the "Layout" menu.
(As a shortcut, you can also double click on the object.)
This will bring up the Layout Definition dialog box, which provides
the user interface for editing any of the graphical characteristics
of the object. Which characteristics of the object are editable
is dependent on the type of the object. At right 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. The set of characteristic
of a graph are substantially different from other layout objects,
more closely resembling the floating palette that is used to stylize
the graph windows. 
There are popup menus showing the X and Y axis parameters,
as well as others to set the graph type and the optional parameters
to governing the look of the resulting plot.
In the case of histograms, it is also possible to
fix the minimum and maximum values on 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's documentation of the graph specification floating
palette.
An additional item found in this dialog is the Control
popup. This will let you specify a graph, or layer in an overlay
graph, to be a control. Controls always show a display of
their original sample, regardless of what sample is currently being
shown in the layout. This provides you a way to create layouts
that show multiple samples, all compared to an original or control
sample.
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The second pane of configuration
in the Layout Item Definition dialog is called Annotate, and governs
the additional annotation that (optionally) accompanies a graph
in a layout.
The first setting is whether the annotation is desired
at all. If you uncheck this box, then FlowJo will not generate
a text box associated with this graph. Assuming that it is
checked, you can optionally have the annotation include
the graph's title, the name of the sample, then name of all the
gates leading to this population (the full name or full path), as
well as statistics showing the frequency and/or the event count.
There is also an additional text box that will let you include any
extra information you may want to display in the layout.
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.
You can request the graph to show its ancestry,
meaning that all the parent populations and gates used to define
this population will be shown as part of this graph. If this
option is chosen, then you can also choose whether to show the ancestry
horizontally across the top of the graph, or vertically along the
left of the main view. You can also choose whether gates that
are defined on this population should be shown. If the graph
is an overlay, then you may choose whether the legend will be visible
or hidden.
Histogram overlays have the additional option of
adding an offset along the Y axis. 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.
Graphs can be resized in the layouts by dragging
any of the corners. The mouse will show the percentage of magnification
as you resize. It is also possible to use the dialog to resize graphs
to a known size or aspect ratio. Typing the values in manually gives
more precise control of the scaling.
To navigate between a graph that appears in a layout,
and the window where its gates are defined, there is a command Open
Original Graph in the Layout 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. There are shortcuts for
this command: from the keyboard: Cmd-R, or with the mouse, by Option-Cmd-clicking
on the graph.
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