The graph window is the window in which FlowJo displays graphical data: contour plots, histograms, dot plots, etc. From this window, you can draw gates to subset the data and select a variety of different representations of the data. To create this window, double-click on any population node within the sample list in the workspace.

The graph window provides much information about the current subpopulation that it displays: cell counts and frequencies (within the sample), any statistics you have requested, and any gates that were computed on the current population. There are controls to navigate the gating tree, so you can automatically go to the graph display that you used to create this subpopulation; you can also automatically display any gate that is created within this subpopulation.

You can select the default graph type for new samples through the preferences dialog. You can change any aspect of the graph by selecting the appropriate menu item under the Graph menu; you can also click on the "i" (information) button to change many features at once. From the preferences dialog, you may also select to display graph windows any of four different styles. Three of the styles provide different set graph sizes with varying amounts of ancillary information... depending on how large your monitor is, you may find one or another optimal. The fourth option is to have a resizeable graph window, in which you can change the aspect ratio and size to virtually any reasonable setting.

All graph windows have controls to switch between the next or previous sample in the workspace window list. When you click on one of these controls, the exact same graph for the next sample which has the same subset is shown (this may mean that intervening samples, which don't have the same gates, are skipped). These controls let you quickly cycle between different samples to compare the graphs. If you hold down the option key while clicking on this control, then all open graph windows are cycled to the next (or previous) sample. In this case, the command is applied individually to each window; thus, if different windows are pointing to different samples, then after cycling they will still point to different samples. You can also activate the next/previous command from the "Graph" menu.

Select a specific topic for more information:

• Graph window styles:  default (large), medium, small, or resizeable.
• Drawing gates
• Changing gates
• Manually entering a gate

The following types of graphs can be generated in the graph window:

You may also wish to look at the pages on copying graphics to other programs and generating publication-quality graphs.