# Plotting Tools¶

## Plotting Chromatograms¶

To produce a chromatogram from simulated data, go to the Tools menu, and select Plot Chromatogram(s) (or ctrl-P), or select the graphing icon located in the toolbar:

All study’s experiment and simulation chromatograms will open in a new tab in the central pane:

If a specific simulation’s chromatography is needed rather than chromatograms from all simulations together, users can right-click on the desired simulation in the Study Data browser, and select Plot Simulation.

The plotting control pane allows to control which experiments and simulations are displayed as well as control, for each experiment/simulation plotted, why type of data to display. By default, only the UV (Protein concentration) is displayed, but users can align below that plot the simulated cation concentration together with experimental conductivities, and/or the pH, each in its own plot:

Note that all of these plots are synchronized, such that zooming in one of them leads to zooming in all of them, so that time alignment is easier. See below about the zoom and other tools.

## Exploring the chromatogram¶

Users can explore chromatograms in details using the tools available in the chromatogram plots:

1. the legend tool
2. the zoom and pan tools
3. the mouse location tool
4. Showing/hiding plot controls

### The legend tool¶

First, it is possible to highlight any of the curves displayed by selecting its symbol in the legend. Note that users can select multiple curves by holding down the Shift key and clicking on all desired curves of interest:

Highlighting and shadowing the same component across simulations may help users to visualize the effect that different values of a given parameter are having on simulations and their resulting chromatograms.

### Zooming and panning¶

The scroll function on a mouse or track pad can be used to zoom in and out of particular areas on the chromatogram. The plot can be panned around, by clicking, holding the mouse and moving it to adjust what portion of the plot is visible. To reset the zoom, press the Esc key.

Clicking in the chromatogram and then pressing Z provides users with a more precise zoom tool, called a box zoom. The mouse becomes a cross, and users can then draw a box around an area of the plot they want to see:

After creating the box, Reveal Chromatography will automatically zoom in on the specified area. To reset the zoom, press the Esc key.

### The position tool¶

Additionally, the chromatogram displays the coordinates of the users mouse in the upper right hand corner of the central pane to support the inspection of chromatograms and other chromatography timeseries:

### Getting controls out of the way¶

Leaves more space for chromatograms, users may want to hide the controls on the left hand side of the screen by clicking on the controls icon located in the application toolbar:

Users can also hide the legend that appears on the chromatogram by clicking on the legend icon in the plot toolbar:

### Building chromatograms from simulation grids and optimizers¶

For information on plotting a the results of a simulation grid, see Plotting the grid’s simulations.

For information on plotting the results from the Parameter Optimizer, see Plotting the optimized solutions.

## Column visualization plot (PRO ONLY)¶

Reveal Chromatography has the ability to create a visualization of the flow of product components through the column with the particle data plot. Reveal Chromatography utilizes the CADET solver to calculate the concentration of the product components over every time slices the simulator solved. The particle data plot can show the concentration of each product component in both the columns and the beads. Use of the particle data plot can help to better understand both column and bead utilization.

To use the particle data plot, navigate to Tools > Particle data animation:

A new, small window will open. Select the simulation from which Reveal Chromatography should produce the plot and press OK.

A new window will open in the central pane. Three heat maps will appear to visualize the concentration of the selected product component at the selected time slice in the liquid phase of the column, the liquid phase in the bead and the bound phase in the bead respectively:

Users can also adjust the time slider at the top of the plot to navigate through different time slices, and see how the select component loads in the column, propagates into and binds to the bead, and finally elutes.

Finally, for any time slice, users can change the component they want to visualize by selecting it from the drop-down menu at the top of the animation plot, to compare how the different components are binding and eluting: