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Module for GEM visualization #56
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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. |
I would implement the functions within the |
Maybe the |
For the batch load function I was wondering if it would make sense to add that to |
The batch load function is already in 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). |
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 |
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. |
All functions were added, can be reopened for future ideas but closed for now. |
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.
ToDos:
comparison.py
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