Getting DeconvExplorer ready for prime time!

[federicomarini]

I am listing here a series of items, gathered by topic, that I think are needed/very worth addressing to get DeconvExplorer ready for its official release.

First a couple of (very) positive things:

• R CMD check is as happy as it can be, with only one note because we have some imports, but that is normal for a package like this interfacing to others
• Also BiocCheck (which we don't need to satisfy but includes some nice extra checks) is relatively happy about the status quo!

General thoughts:

• We could think of being anti-generous in including dependencies, like “do we really need bbplot” or are we fine with an empty-ish ggplot theme, this kind of things - my suggestion: reduce dependencies if we can! Happy to see what is used from each "exotic" package dependency and see what we really need from each.

Must do:

• @czackl add your ORCID in the DESCRIPTION

DOCUMENTATION OF THE APP:

• We would ideally show some example files, maybe with a modal dialog popup? Unclear data requirements as of now, people like screenshots vs text [ShouldDo]
• some help could be beneficial to explain what does what [ShouldDo]

USER EXPERIENCE:

• Keeping users informed that we do things: info notification WHILE loading, and one deleting the progress and saying it is all cool [ShouldDo]
• UI design: [ShouldDo]
  • Avoid overload of content with some collapsible elements?
  • Larger, otherwise colored deconvolute button - it is the main one! a little more in the center?
  • deconv table:_ is the first column really a “gene”?
  • Explain at least once what to do in each part of the app
  • The load/add/remove buttons are not very intuitive. What about a menu from where we can select one or multiple options?
  • Some visualizations throw an error (e.g. 1 method, scatter, cell type).

Open Qs & Misc items

• What is the difference between “Deconvolute” and “Deconvolute all”

• What is the difference between “Deconvolution method” and “Signature method”? Is this really relevant? How we can change the latter

• If feasible, it could be helpful to have an information button (i) next to the menus to load data or select the parameters to explain to the user what is expected, the format, etc. [NiceToHave]

[czackl]

Added the ORCID! Thanks for the efforts, pretty busy with spacedeconv currently 🙈

[federicomarini]

Perfect.
Will try to get an estimate of what are the "really needed dependencies". Somewhat data (=code) driven...

[federicomarini]

Slimmed up the dependencies - I would say we are in good shape there now