The Plot panel manages the creation of plots and allows to revisit plots that are stored in the database.
Click the button to open a wizard that will guide you through the process of creating a new plot. First you'll be prompted whether you'd like to plot the results of a single simulation setup, or whether simulation group should be used to combine multiple simulation setups. Groups differ from single setups in how the data is being handled, when selecting a single setup, you'll be able to plot any combination of time, observations and parameters against each other. When using a group the data will be pre-processed to select a single observation at a single point in time. The values defined in the simulation group will be added as an additional dimension to the plot. Once you've selected the simulation or group, you'll have the choice of different representation of the data:
- Single plot
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Two variables, such as a concentration and time are plotted against each other. Parameters or other variables can be used to color the plot symbols.
- Multiple Plots
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Two variables, such as a concentration and time are plotted against each other. Additionally all pair-wise combinations of parameters are plotted in a linked display. Selecting points in the primary plot using the and dragging will select the corresponding points in the parameter plots and vice versa.
- Factor Mapping
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Two variables, such as a concentration and time are plotted against each other. Additionally empirical cumulative density functions (ecdf) of parameters are plotted in a linked display. Selecting points in the primary display will cause a simultaneous selection of parameter values. If points at different times are selected a parameter value will only be part of the selected set if it is selected at every time at which at least one point is selected. Points at selected times, that themselves are not selected are shown in blue. Using Shift+ allows to select multiple regions by adding to the current selection, points can be de-selected using Ctrl+.
Once points are selected, the ecdf of the selected and the unselected parameter values will be added to the display. Additionally the set of displayed parameters may change. In order to keep the plot from readable in the presence of many parameters only parameters whose selected and unselected distributions differ significantly are displayed. If the number of parameters is less than four, and non -significant parameters are available, non significant parameters will be added to the plot to fill up the remaining space. The p-values displayed above the ecdf are the uncorrected -p-values for the two sided Kolmogorov-Smirnov test. This allows to gauge the influence of the parameters on the selected behavior. In the example, the selected points are strongly influenced by the parameter "Galpha auto-GTPase" all selected points occupy low parameter values. The next parameters have little influence. Both their ecdfs are similar.
Once you've selected a plot type, proceed to the next page.
Here you can change which quantities are plotted, the appearance of the plot and how data is transformed or summarized before plotting. A useful tool is under the selections box, checking the box will expand a panel for loading and saving selections, as well as their intersections and unions. The "load" button will replace the current selection, The "compare" button can be used in conjunction with factor mapping to display additional ecdfs for comparison with the current selection. Click to save the plot. Clicking next will allow you to add descriptive text to the plot.