Graphs¶
The Graphs panel is the left-hand side of the Parameter Explorer. It holds an array of small charts, each plotting one or more model variables — and, on the same axes, any experimental data associated with them.
Managing graphs¶
The toolbar above the array:
| Control | Does |
|---|---|
| Add | Create a graph |
| Remove | Delete the selected graphs |
| Ref Plots | Show or hide curves from the reference parameter set |
| All Graphs | Show every graph, or only the ones matching the current filters |
| New Window | Open a separate graph window (see below) |
| Add Filter | Narrow the array to graphs carrying a chosen tag |
| Text Search | Narrow the array to graphs whose plots match a word |
Each graph has a visibility checkbox and an Add Tag button. Tags are free
text — flux, for the paper, does not fit — and they are how you keep
thirty graphs manageable: tag them, then filter.
Configuring one graph¶
Right-click a graph and choose Edit to open Edit Graph Settings:
- Title, and labels, minimum, maximum, and Log Scale for each axis;
- Type — Time Series or Parametric (one variable against another, for phase-plane plots);
- a Plots list — the model variables drawn — with Add and Remove;
- an Experimental Data list — the measurement and data set drawn — with Add and Remove.
Each plot has a colour you can change.
The rest of the right-click menu: Copy and Save As for getting a chart into a manuscript, Show Only This Graph / Show All Graphs for zooming in on one, Reset Zoom, and Data Browser for the numbers behind the picture.
Your graph layout is saved per MOE by the Parameter Explorer's Save button, so it is there next time — and for anyone else who opens the MOE.
Graph windows¶
New Window opens a second graph window on the same MOE. It shows the same graphs — edit one in either window and both update — so its first use is simply seeing more charts at once, on a second monitor if you have one.
It is also where the more analytical plotting lives. It has a Log Y checkbox, tag filters, and three display modes.
User mode¶
The graphs you have configured yourself, exactly as in the Parameter Explorer's own panel. This is the ordinary mode.
Selected mode¶
Plots whatever is currently selected in the Model Realization's diagram. Click a state there and its trajectory appears here; click a process and you get its flux. Nothing to set up, which makes it the best way to walk through an unfamiliar model.
Two things are needed for anything to appear: a selection in the diagram, and a MOE that has been simulated. The window says which one is missing.
Cursor mode¶
Plots the selection in its network context.
For a selected state, it draws five panels:
| Panel | Shows |
|---|---|
| The state itself | Its trajectory |
| Influxes | The fluxes of every process producing it |
| Outfluxes | The fluxes of every process consuming it |
| Precursors | The states feeding those influx processes |
| Postcursors | The states produced by those outflux processes |
For a selected process, it draws the process flux together with its Reactants, Modifiers, and Products.
As with Selected mode, the MOE must have been simulated before there is anything to plot.
This answers, in one glance, the question you actually have when a concentration behaves oddly: what is putting it there and what is taking it away? — and it follows the model as you edit it, including states and processes you have not committed yet.
Note
Cursor graphs follow reactant and product roles only. Modifiers are excluded from precursors and postcursors, since a regulator neither donates nor receives material.
Data on graphs¶
Experimental data is drawn as points against the simulated curve for the same variable. If your data is not appearing, check that the measurement has a Variable set — see Measurements and data.
Data points can be selected on a chart, which highlights the corresponding row in the Data Browser and in the weights editor — useful when one outlier is dominating a fit.