Frequency Histogram Window

A frequency histogram window displays a plot that shows the frequency with which each reaction step and transfer step in the reaction scheme is chosen to advance during the most recent simulation.

Prior to creating a frequency histogram window, you must execute a simulation with the "Track selection frequency of each step" option enabled in the Application Options Dialog.

To create a frequency histogram window:

  1. Click the right mouse button over an empty area of a scheme diagram
  2. Select the Show Selection Frequencies of Entire Scheme menu item from the context menu.

    A frequency histogram window appears:

Interpreting the Frequency Data

During a calculation, the simulator randomly selects one step from all reaction steps and transfer steps in the reaction scheme, using probabilities weighted by the instantaneous rates of each step. On each iteration of the simulation loop, the selected step is allowed to proceed, the state of the system changes incrementally, and probabilities are recalculated. In this stochastic method, steps with large relative rates will tend to be selected more frequently.

A frequency histogram window allows you to examine how frequently individual steps in your reaction scheme are selected. The frequency data are presented as two graphs where the horizontal axis covers the range of frequencies of selection during the most recent simulation. On the left plot, the vertical axis shows how many steps are selected within over a span of frequencies; the right plot shows the fraction of the overall simulation execution time that is spent in selecting steps over a span of frequencies. The histograms of reaction steps are shown in blue and the histograms of transfer steps are shown in red.

As an example, consider the "TBOC Image 2D 4000 nm pitch" reaction scheme from the examples distributed with Kinetiscope. That scheme uses 2440 compartments and 4636 transfer paths and includes a total of 23912 reaction steps and transfer steps. The figure above depicts frequency histograms for how often each of these steps is selected. The left graph shows that a large number of steps are never selected under the specified reaction conditions (these have frequency of selection equal to zero), and in general that reaction steps are selected more frequently than transfer steps. The right graph shows the "time cost" for the each step; this shows that most of the calculation time is spent propagating the chemical reactions rather than in transport of species between compartments.

Changing the Plot Scales

Two different mechanisms are available to change the scales and limits of the plot axes.

Zoom with the Mouse

You may select a region of the visible plot to be expanded using the mouse. You may zoom in repetitively in this way to view detail in the plotted data.

To zoom in to a region:

  1. Press and hold down the left mouse button at one corner of the region.
  2. While holding down the mouse button, move the mouse cursor to the opposite corner of the region. A "rubber-band" rectangle bounds the region to be displayed.
  3. Release the mouse button. The graph is rescaled to show just the selected region.

Rescaling the Axes

You also may set the minimum and maximum limits of both scales by typing in precise numeric values.

To do a precision rescaling:

  1. Double-click the left mouse button over the title or labels of the axis you wish to rescale.
  2. A Change Scale Limits Dialog opens. Type the minimum and maximum values for the range you wish to display.
  3. Click OK. The dialog closes and the graph is rescaled to your specification.

Text View

You may display all the numeric data that comprises the current graphical view as a text-based table. You use the graphical view's context menu (see below) to switch to this display. The table may be exported to a text file.

Context Menus

Context menus for both the graphical and text views of this window are accessed using a single click of the right mouse button.

The context menu of the graphical view provides the following actions:

Modify...
This action opens a simple dialog where you may change which parameters are plotted and modify other plot attributes.
Copy
When this menu item is selected, a bitmap image of the plot is placed on the system's clipboard. This image may be pasted into other applications.
Export to Image File...
When this menu item is selected, a File Save Dialog appears that allows you to save an image of the plot to a disk file. The image is saved in Portable Network Graphics (.png) format.
Show in Text Format
Selection of this menu item switches the window from graphical format to a tabular text format.
Zoom In
This menu item is enabled after you have used the mouse method to change scaling. This action zooms in to a previous scaled view.
Zoom Out
This menu item is enabled after you have used the mouse method to change scaling. This action zooms out to a previous scaled view.
Reset Zoom
The menu item is enabled after you have used the mouse method to change scaling. This action restores the initial scale.
Show All Data
This action resets both scales to ensure all data points are visible.
Show Steps at Cursor
Selection of this menu item toggles the on-screen display of a list of steps that comprise the histogram datum points at the cursor's current location. Up to ten reaction steps and ten transfer steps are displayed on the plot near the cursor.

The context menu of the text view provides the following actions:

Export to Text File...
When this menu item is selected, a File Save Dialog appears that allows you to save the tabular text to a disk file.
Show in Graphical Format
Selection of this menu item switches the window from text format to graphical format.
Select All
This action selects all text for a pending Copy operation. You may select a portion of the table to copy by holding down the left mouse button while moving the mouse cursor over the text.
Copy
When this menu item is selected, a copy of any selected text is placed on the system's clipboard. This text may be pasted into other applications.
Zoom In
Selection of this menu item increases the font size of the text table.
Zoom Out
Selection of this menu item decreases the font size of the text table.