# Plotting Time Series Data

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:

- Show - If the check box is selected, then the item will be plotted. Clicking on a cell will toggle the state. Left/right clicking on the column header will select/deselect all of the items.
- Std Dev - This column is only visible when plotting statistics. If selected, a standard deviation bar will be shown at each frame. Left/right clicking on the column header will select/deselect all of the items.
- Line Color - Clicking on a cell will bring up a color palette dialog. Left clicking on the column header with assign a different color to each selected item using a range of hues. Right clicking on the header will set all of the line colors to black.
- Style - The line style may be solid, dashed, dash-dot, or dot. Clicking on cell will activate a drop-down box. Left clicking on the column header will cycle between the styles for the selected items. Right clicking will reset all of the line styles to solid.
- Width - The line width is a positive integer. Clicking on a cell will activate a spinner editor. Left/right clicking on the column header will increment/decrement each of the widths.
- Marker Style - A variety of marker styles are available. By default no marker is plotted. If a marker style is selected it will appear at each frame. Click on a cell to activate a drop-down box of styles. Left click on the column header to cycle between the styles for the selected items. Right click to turn off markers for all items.
- Size - The marker size is a positive integer, which may be edited for each item. Left/right clicking on the column header will increment/decrement each of the sizes.
- Face Color - The face color is the color of the interior portion of the marker. Clicking on a cell will bring up a color palette dialog. Left clicking on the column header will color the selected items by hue. Right clicking will set all of the colors to black.
- Edge Color - The edge color is the color of the boundary of the marker. It may be edited in the same manner as the face color.
- Edge Width - The edge width is positive integer that may be edited like the line width and marker size.
- Legend Label - Left clicking on the column header will set these labels to the row labels, which are either the species or reaction identifiers. Right clicking on the column header will clear the labels. By clicking on a cell one may edit a single label.

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.