[JOSS Review] Update overview graphics

[hechth]

The main diagram showing the workflows could be extended with something closer to the code, showing the individual operations and data flow. I thought about something like this. If you agree, I can share the document and we can make a refined version of this, maybe also including links to the actual function documentation etc.

[rickhelmus]

Hi @hechth

Many thanks for this diagram and also for the other feedback! The diagram looks very clear and definitely something I would like to include. I just returned from Holidays and still catching up... but hopefully I can work on the issues and give a more thorough look at the scheme later this week.

Thanks, Rick

[hechth]

Hi Rick,

sure, take your time -,and please don't feel overloaded given the number of issues etc. I created - most of them are very minor things. I will also need a bit more time to finish the review - just reach out if something is not clear or you'd like some support from my side with certain things.

Best, Helge

[rickhelmus]

Hi Helge,

Thanks again for the scheme, I am still quite happy with it! :-) I think it would be a great addition to the beginning of the Handbook, and perhaps also something to include to main package reference documentation page.

It covers nearly all workflow steps now. Obviously, there is no room for all the data handling functionality too, but if we could somehow include links to the reference docs this will makes things very easy to explore. The only step missing now is pretty minor: this is about using adduct and isotope annotations from components with selectIons() to prioritize adducts/isotopes and add annotations to remaining feature groups. As this only concerns components with adduct/isotope annotations (there are several other types of components in patRoon), perhaps the diagram could show an additional data block for these components (unfortunately they are currently not in a different S4 class) and connect it with a dotted line to the featureGroups. Although I am not sure if things get too crowded then.

If you would be fine with briefly sharing how the diagram was created I can also poke around myself.

Tagging @schymane here in case you also have some thoughts :-)

Thanks, Rick

[hechth]

I created the graphics using draw.io - I attached the file I posted above as an XML, I think you should be able to import it (under Import -> Device) and make changes. If this doesn't work I'll send you a link with the shared document from GoogleDrive via email.

I agree with your suggestions, I think adding links would be great (I didn't do that so far since links don't carry over into PNGs - I still didn't figure a way how to put graphics from draw.io nicely into PDF or pptx files, maintaining the links etc. - I think it works as SVG or HTML), also adding the functionality that I missed would be good.

patroon.zip

[rickhelmus]

Thanks! The import works.

To include URL links and to (hopefully) make it more easy to maintain I started experimenting with graphViz

Not quite there yet... the layout with so many connections is particularly tricky.

[rickhelmus]

More progress!

Next step is auto URL linking :-)

[rickhelmus]

Alright, the URL links are now in and after some more tweaks the graph is now in the Handbook.

[hechth]

This is amazing!