Plot Files

Plot files are textual descriptions of a given plot in JSON format. Remember, a plot within the program is not separately stored in a file; it is saved with the project, thus a plot file must be explicitly created, and will exist outside the project. There are two principal reasons saving a plot this way: for re-use in a different project, or to access the commands/keywords used to build the plot (see TOPIC).

Inclusion in a Model

There is one method for opening a plot file in the current project:


There is no command to open a *.plt file into a project; the operation is performed only through interface tools.

Save a Plot File

There are two methods for saving a plot file:

  • from the “Save” button ( save ) on the toolbar of the plot to be saved

  • from the File —> [plot name] —> Save As... menu command (where [plot name] will be the name of the active plot, as shown on its title bar)


There is no command for saving a *.plt file; the operation is performed only through interface tools.

Plot Files and Plot Data Files

The program provides two methods of storing a plot. A plot file, as described here, is a text-based JSON description of the current plot. The description found in the file will be identical to the description found in the project file (*.prj) for that plot. A plot data file contains the complete set of commands used to create a given plot. Neither file type is created automatically by the program; either must be explicitly created and saved by the user.

From a functional perspective, there is significant overlap between saving a plot (*.plt) file and saving a plot data (*.dat) file.

  • Either are a way of storing a given plot so that it exists independently of the project (see above).

  • Either may be used to re-build in one project a plot that had previously been built in another.

  • Either can be interpreted (*.plt) or read (*.dat) to see what commands went into construction of a given plot.

  • Either, if brought to a new project, may or may not make sense relative to the current model state of the new project.

One might preferentially use one instead of the other for the following reasons.

  • Plot data files are, like any *.dat file, call-able with the program call command. Consequently these can be folded into the call stack for a model run; plot files cannot. If plot construction during a run is needed, these will be preferable.

  • If on-the-fly plot manipulation — that is, scripting the plotting process with FISH or Python — will be a part of a model run, users may find it easier to use plot files rather than data files to identify the switches they wish to manipulate in the scripting process. The c plot commands for creation and manipulation plots are provided in this documenation, but the commands for configuring the appearance of plot items are not. This is why a user might have an interest in using either plot file or a plot data file to see them (see topic Command-Driven Plotting Workflow for further information).