Vignettes and documentation

[lmsimp]

A new getting started with pRolocGUI vignette

• What is pRolocGUI used for
• Update screen shots of Apps
• Walk through examples for each app

Other

• Documentation - one .Rd file for all Apps
• Talk to @lgatto about new videos for apps once above done - see issue Documentation #33

[lmsimp]

Will need to update/replace this

[lgatto]

My plan was to automatically build to vignette as the README file.

[lmsimp]

@lgatto I am re-writing the vignette at the moment. What to do about plotMat2D?

[lgatto]

Is plotMat2Ds functionality not addressed in the official apps? I would keep it for now, but not export it yet. Let's see what is missing once the overview vignette is written.

[lmsimp]

Is there any reason why the current pRolocGUI vignette is html and the vignettes for pRoloc and MSnbase are PDFs?

[lgatto]

Mainly historical. But I prefer to keep it html, as it can be more easily read online. Also, I would prefer if you used BiocStyle.

[lmsimp]

@lgatto Update:

• The vignette is now up-to-date but explaining the compare application is tricky as it's quite a complicated application and there is already documentation. At the moment I refer to this other vignette, but this old vignette needs updating if we refer to it. What to do about legacy and docs? - see legacy model #31
• I think the best option is to re-write the compare app it so it's pretty much the same as the PCA app but with two plots. I can open a new issue for this and we can discuss?
• With regard to writing an application note, I think we need to think about some nice use cases for each e.g. hyperLOPIT data, for the profiles app would be nice to show how to discriminate between clusters and peroxisome and mitochondria would be good for this as they are overlapping in PCA etc.
• Also, we could add your movies as an app. This is cool, but you comment that it may not be useful in practise... however, this may be useful for someone who wishes to show dynamic re-locations of their experiment in a presentation.

[lgatto]

At the moment I refer to this other vignette, but this old vignette needs updating if we refer to it.

Yes, that's fine. I would like to get all the other apps/docs ready before removing anything.

I think the best option is to re-write the compare app it so it's pretty much the same as the PCA app but with two plots. I can open a new issue for this and we can discuss?

Ok for issue, but let's make sure all other apps are 100% before starting this new one.

Ack your points re application note. Not sure why you would want to turn the animations into apps?

[lmsimp]

Add plot2Ds and move2Ds on the end of the vignette.

As far as vis in pRoloc goes we have:

• plot2D
• plotDist
• plot2Ds
• move2Ds

Can you add to the list @lgatto want to re-cap on Monday what we have already in pRoloc

[lgatto]

I think the list is complete. What I really wanted to emphasise in this visualisation vignette were basic visualisation principles such as what are PCA or profile plots good for (this is now explained in the GUI vignette) and describe the different dimensionality reduction methods available. The latter could probably go in the plot2D documentation at this stage.

The last two functions are not described anywhere, so it might be good to briefly mention them after the compare app. I don't think we should go into too many details at this stage.

[lmsimp]

move2Ds does not work in RStudio but seems to work fine when using R from the command line where XQuartz is launched for graphics. This of course does not matter for today, but is something we should fix.

Also, where and what is the name of the function that you have written to show all dim reduction plots at once?

[lgatto]

move2Ds does not work in RStudio but seems to work fine when using R from the command line where XQuartz is launched for graphics. This of course does not matter for today, but is something we should fix.

Could you open an issue in pRoloc for this?

Also, where and what is the name of the function that you have written to show all dim reduction plots at once?

See SpatProtVis.