Module for GEM visualization

[famosab]

Is your feature request related to a problem? Please describe.
Many manuscripts cover visualization of models like bar charts with numbers of metabolites.

Describe the solution you'd like
RefinGEMs could profit from a small module that holds scripts that enable fast creation of such figures or at least a basis on how to start visualization.

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ToDos:

• how to handle multiple models
• how does this relate to comparison.py
• SBO visualization
• bar charts for multiple models
• venn diagrams for all entities
• growth rate heat maps

[GwennyGit]

This idea sounds great. Adding additional scripts to get Venn diagrams as visualisation of model comparisons might be great as well. To handle more than 4 models a comparison bar chart could be used instead of the Venn diagrams.

Regarding the implementation we could compare our two scripts with which we created the Venn diagrams so far.

Here is my script model_data_visualisation.py.

[famosab]

I would implement the functions within the comparison module since most of the visualization only makes sense when working with multiple models. A heatmap which shows growth rates for a single model could be either added to the comparison module or the growth module.

[GwennyGit]

Maybe the OBOParser mentioned in comment draeger-lab/SBOannotator#1 could be useful for the SBO visualisation.
I think the visualisation of the growth rates for a single model would make sense in the growth module. However, a function to obtain the amount of entities might make sense not only for multiple models but also for a single model. This would then lead to two visualisation functions being in growth and similar functionality for multiple models in comparison. Would it not be better to have a module containing all visualisations? 🤔

[GwennyGit]

For the batch load function I was wondering if it would make sense to add that to io as soon as we have that module.

[famosab]

The batch load function is already in load so it should be transferred either way. I will do the migration to io as soon as we merged polish.

Separate module depends on how we view visualization. I thought of it more as a way to show what refineGEMs already reports and thus it makes sense to include the respective functions within the respective modules. But maybe that is confusing? However I think that the ideas for visualization that I had so far are not complicated either so migrating them to another module should not be an issue anyway. We have the entity number reporting function already so it's just a question on where to locate the actual visualization functions. I was hesitant to add yet another module since it makes using refineGEMs within a Python script more complicated (from my point of view).

[GwennyGit]

Regarding the visualisation, if the user wants to use refineGEMs within a python script is it not easier for the person to locate visualisations if there is a module called visualisation even though there are a lot of modules? 🤔

[famosab]

So far I created all visualizations either in investigate (single model) or in comparison (multiple models). And the styling is not the best. I could either initialize matplotlib with PARAMS we decide on or (what I saw when I used the functions locally): the user loads matplotlib with their specifications and then it fits.

[famosab]

All functions were added, can be reopened for future ideas but closed for now.