Open the file examples/cain/WilkinsonSMfSB/autoreg-2-1.xml.
Then select all of the species and reactions in the recorder panel.
(All of the species are selected by default. Switch to the Reactions
tab and then hit the
button to add all of the reactions.)
Next generate 10 trajectories using the defined model and method
by entering 10 in the Trajectories field and hitting the launch
button
.
Then click the plotting button
in the simulation output panel. This will bring up the plot
configuration window shown below.
The plot configuration window consists of two tabs, one for time series output and one for histogram output. Since we just generated 10 trajectories recorded with time series data we will work with the former. At the top of the window is a drop-down box for choosing the simulation output to plot. The output is described by the model and method that was used to generate it.
Below the output selection are two rows of radio buttons. In the first row one selects whether to plot species populations, cumulative reaction counts, or binned reaction counts. The binned reactions counts are the number of reaction events that occur between the time frames. Note that only the species and reactions that were selected in the recorder panel when the simulation was run are available for plotting. By default all of the species are selected and the reactions are not. In the second row of radio buttons, one selects whether to plot trajectories, the mean (and optionally the standard deviation shown as an error bar), or the standard deviation.
Note that for simulation output that records all of the reaction events the Binned Reactions radio button is disabled as there are no fixed time frames. Also the statistics radio button is disabled; one may only plot the trajectories.
Next is a grid which lists either the species or reactions in the column headers. The row headers describe configuration options for the lines which plot either the trajectories or statistics. One may edit the grid cells individually or click on the column headers to modify values for all rows. The columns have the following behavior:
At the bottom of the plot configuration window one may select whether the legend will be displayed. For this legend one may also choose the font size and location. Next one may customize the size of the tick labels on the axes. One may enter the title and axes labels if desired. For these one may select the text color by clicking the color button or change the text size by choosing from the pull-down menu.
When data is plotted, a domain will be chosen that contains all of the data points. You may change this behavior by explicitly setting the lower and upper limits of the X and Y axes. Note that you may enter any subset of these four limits. Any omitted limits will be automatically calculated. Finally, one may specify the size of the plotting window.
Below is a plotting window for the auto-regulatory system. The legend has been placed in the upper left corner. We have added a title and axes labels.
Note that there is a toolbar at the top of the plotting window. Positioning the mouse pointer over these will bring up tool tips which describe their functionality. The most important feature is the last button, which is used to save the figure to a file. Depending on the version of the matplotlib library installed, not all file formats may be supported.
See the Examples chapter for a variety of sample plots.