Allow species in `yValues` of the visualization table

PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

https://petab.readthedocs.io

MIT License

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Allow species in `yValues` of the visualization table #569

Open paulflang opened 8 months ago

paulflang commented 8 months ago

Which problem would you like to address? Please describe. Atm it seems like only observables can be plotted on the y axis. It would be nice to also be able to plot species.

Additional context This would be helpful to visually check

if the behavior of non-observed species for a given optimization result seems biologically reasonable
how species differ between experimental conditions
how species differ between different optimization results, etc.

dweindl commented 8 months ago

Agreed, this would be quite helpful. When changing that, we should probably just allow any model entity with globally unique identifier (e.g., parameters, compartments).

dweindl commented 7 months ago

I think for the current way of plotting based on simulation files we could allow for pretty much everything that is present in that file. It would be an abuse of observableId, though. For practical purposes, I think it would already work if you add your species to a simulation file and let libpetab plot it. There is currently no validation for simulation files.