Graph Window

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 create subsets of 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.

Click on the image at the right to learn more about each tool.

The graph window provides much information about the current subpopulation that it displays: cell counts and frequencies (percentage of total 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.

Select a graph type from the Options menu. Select Save State to Preferences from the Edit menu. You are saving your preference for that graph type. Each time you open a new graph, your saved graph type will be displayed.

All graph windows have controls to navigate among the samples in the workspace window list. (Arrows, upper right.) These controls let you quickly cycle between different samples to compare the graphs. When you click on left and right arrows, the exact same graph for the next or previous sample which has the same subset is shown. (This may mean that intervening samples, which don't have the same gates, are skipped.) The middle diamond buttons open a list of samples from which to choose the parent of the subpopulation you are viewing, or to display that parent. You can also activate the next/previous command from the Graph menu at the top of the monitor

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Axis Labels

A graph's axis labels are drop-down menus. Left click on an axis label to open a list of that population's parameters. Select from that list and that parameter is displayed on the corresponding axis. If you or your cytometer have applied a compensation matrix to the population in the graph, those compensated parameters will also be available for selection. Event Number is also avalable as a parameter by checking the box in the Options menu.

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When compensated parameters are displayed, the Display Transformation button appears beside the axis label. Click it to add a transformation calculation to the axis. For more details, click HERE.

Select a specific topic for more information:

• Graph window
• 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.