When you open the disclosure triangles at the bottom of the graph window, the following options are shown. From this window, you can modify the attributes of the current graph (or currently-selected gate). The first time you are shown this window, the bottom three"sections" are hidden; click on the triangles to reveal them.

Graph Type pulldown will let you select how to display your data. The options are Density, Contour, CDF, Histogram, Dot Plot, Zebra and Pseudocolor.
For Contour plot option, you can choose how many events should fall into each line. The choices are 10%, 5% and 2%. You may also wish to display Outliers (last N% of events shown as dots)
Some plots may be Smoothed. This setting affects everything except dotplots and CDF graphs.

Gate Events Inside option toggles wether the region you drew is intended to enumerate cells inside it or outside it.
Draw Tinted will let you fill your regions with the specified color.

The statistics pane shows a brief statistical summary of the graphed population.

Use the gating tools () when you want to create a new gate of a particular kind. The quadrant tool is a special case: it creates four gates (click here for more information).

Graph Options: The first disclosure triangle defines the graph type and options to display the data in the graph window. This includes vertical (Y-axis) scaling for histogram and CDF univariate plots.

Active Gate: These options are enabled whenever you have a single gate selected in the graph window. Here you can choose to gate for events inside or outside the gate. If remove the check mark and choose to display events outside the gate, this is equivalent to a NOT gate when using Boolean expressions. You can choose to draw the gate in a different color than the default. Tinting the area inside the gate only alters the drawing of the gate; it does not change the colors of any events (dots) on any of the graphs.

Statistics: Click on the sigma button to add statistics to be calculated on population you have displayed in the graph window.

Gating Tools: The gating tools at the top of the graph window allow you to create a new gate of a particular kind. The quadrant tool is a special case: it creates four gates (click here for more information).

Finally, the bottom section is enabled whenever you have a single gate selected in the graph window. Here you can choose to gate for events inside or outside the gate, and choose to draw the gate in a different color than the default. Tinting the area inside the gate only alters the drawing of the gate; it does not change the colors of any events (dots) on any of the graphs.

The preferences dialog specifies whether you must click on a gate tool to create a new gate; or whether FlowJo will "auto-select" a gate tool when you click in a graph window.

If you leave the Options, Active Gate or Statistics disclosure triangles open (even if you close the graph window), and you apply this gate to a group - the equivalent subsets from other samples that are subsequently displayed will have the disclosure triangles open.