The Graph window is the window in which FlowJo displays graphical data. To create this window, double-click on any population node within the sample list in the workspace. From this window, you can:
- Display contour plots, histograms, dot plots, etc.
- Draw gates to create subsets of the data and select a variety of different representations of the data.
- Navigate the gating tree.
- View information about the current displayed subpopulation.
Mouse over the red dots for more details.
The File menu:
- Close: Closes the active graph window.
- Close All Windows: Closes all open graph windows.
- Reset All Graph Windows Size: Resets all graph windows to the default size.
- Save As: Opens the Save Graph Window window and allows for the saving of the graph to various image formats.
- Export To App: Opens the Save Graph Window window and allows for the saving of the graph to various image formats.
- Page Setup: Opens the Page Setup window and allows for the adjusting of options for printing your graph.
- Print Preview: Opens the Print Preview window and allows for the viewing and adjusting of the graph's look before printing.
- Print: Prints the active graph window.
The Edit menu:
- Undo: Undoes the most recent action.
- Clear: Deletes the selected gate.
- Copy Picture: Converts the active graph into a picture and copies it to the clipboard.
- Copy Picture With Gates: Converts the active graph and its gates into a picture and copies it to the clipboard.
- Copy histogram As Text: Converts an active histogram into text and copies it to the clipboard.
- Copy Statistics: Converts the statistics of the active graph into text and copies it to the clipboard.
- Copy Gate: Copies the active gate into the clipboard.
- Copy To Layout Editor: Copies the active graph into the Layout Editor.
- Paste Gate: Pastes the most recently copied gate.
- Add Statistic: Opens the Add Statistic window and allows for the adding of statistics and parameters to your sample.
- Preferences: Opens the Preferences window and allows for the configuration of FlowJo to your liking.
- Save State To Preferences: Saves the state of the active graph as the default state for all subsequent graphs.
The Graph menu:
- Transpose Axes: Swaps the values of the X and Y axes.
- Derive Parameter: Opens the Derived Parameter Definition window and allows for the definition of custom parameters.
- Manually Enter Gate: Opens the Manual Gate Entry window and allows for the definition of custom gates.
- Make Movie: Opens the Movie Specification window and allows for the conversion of graph data into movie format.
- Hide/Show Options: Conceals or exposes the expandable categories at the bottom of the window.
- Gating Tool: Optionally select gating tools from this menu: Arrow, Rectangle, Polygon, Ellipse, Range, Quad, or Autogate.
- Default Tool: Sets the default active gating tool for all future graphs: None, Rectangle, Polygon, or Ellipse.
- Sample Properties: Opens the Sample Properties window and displays keywords and parameter/stain information about the sample, as well as its compensation matrix.
The Display menu:
- Graph Type: Optionally select graph types from this menu: Contour, Density, Zebra, Pseudocolor, Dot Plot, Histogram, or CDF.
- Graph Options: Optionally set graph options from this menu: Contour Levels, Smooth, and Show Outliers.
- Show Grid: Toggles a grid overlay in the graph.
- Use Scientific Notation: Toggles scientific notation.
- Use Large Dots: Toggles larger viewable dots when viewing dot plots or outliers.
- Show Gate Frequencies: Toggles the view of gate frequency statistics in the graph.
- Show Gate Medians: Toggles the view of gate medians in the graph.
- Show Uncompensated Parameters: Toggles the view of uncompensated parameters in the graph.
- Show Event # Parameter: Toggles the view of the event parameter in the graph.
- Keep Quad Gate Annotations in Corners: Shifts quad gate annotations to the corners of the graph.
The Go menu:
- Workspace: Navigates to the Workspace window.
- Parent: Navigates to the graph window of the parent population.
- Child: Navigates to the graph window of the child population.
- Next Sample: Iterates forward through the available samples in the graph window.
- Previous Sample: Iterates backward through the available samples in the graph window.
- Previous X: Iterates backward through the X axis parameters in the graph window.
- Next X: Iterates forward through the X axis parameters in the graph window.
- Previous Y: Iterates backward through the Y axis parameters in the graph window.
- Next Y: Iterates forward through the Y axis parameters in the graph window.
