Feature/DIMS refactor GenerateViolinPlots

[ALuesink]

The refactor of GenerateViolinPlots:

• code to functions
• added unit tests

[rernst]

First of all lots of work done, good job! I feel like there is room for improvement, some general thoughts:

1. Many parameters have names like metab_interest_sorted. In the context of a function, it’s not relevant whether the input is “of interest” or “sorted.” Use neutral, descriptive names that reflect the data type or role.

2. Several functions are named after their use case rather than their functionality. name functions based on what they do, not where they are used.

3. When breaking function calls across lines, maintain a consistent style. Preferred format:

Rfunction1(
   function_2(param_a),  
   param_b,  
   param_c,
)

4. There is no error catching for missing files or invalid paths. Currently, the code will crash, making debugging difficult.

5. There seems to be a lot of ad-hoc data transformations. It feels like the DIMS application is missing a standardized data format for saving and reusing data between steps.