Laurent Gatto
Laurent Gatto
@sgibb - trying to catch up (still travelling, until next week). A few thoughts - Following `mzIdentML` conventions, as mentioned by @adder in the post above could be a winning...
> You also have to be able to specify where the variable modificiation is positioned. Eg. if you have a sequence with 2 serines. You can have a Phospo group...
Excellent initiative! I have now given you admin rights to the CPU repo.
> Question is whether we should also harmonize the use of `ggplot` or base plotting. Although `ggplot` is powerful, I'm still a fan of the base R plotting functions. I...
> You think parameters `rt` and `mz` are required? We could also drop these leaving the task of subsetting by rt and mz using `filterRt` and `filterMz` to the user....
Indeed. So I was thinking in somehow checking that the `MSnExp` that is passed has a *sensible* retention time and mz range (or has been filtered beforehand) and, if not,...
@chasemc - indeed, we all agree with you. We might revert back to base plotting in some cases where `ggplot2` isn't used to its full potential.
In the framing of rationalising MS data plotting, it will also be worth considering unit tests using the [`vdiffr`](https://github.com/r-lib/vdiffr) package.
@jorainer @sgibb - at the last EuroBioc2019 conference, there were some discussions about MS plotting. Is this issue still relevant/useful?
Unfortunately, I can't seem to transfer this issue to `Spectra`. Will keep it for now and will copy the info into a new one.