Outstanding issues for HDX streamline features

[broncio123]

Loose ends (bugs and potential enhancements)

• [x] Find out why Manhattan plots fail for Case Study No. 3 https://github.com/ococrook/hdxstats/blob/db12beb29f13262013ec4059c6025f74dfc2cf36/vignettes/tutorial-streamline.Rmd#L369-L372 . Assign: @broncio123

• [x] Find out if colData(qDF) and rowData(qDF) can be implemented to store peptide Start and End residue numbers, instead of qDF@metadata. Assing: @broncio123

• [x] Replace some methods with more robust versions of them, e.g., seq_len(5) instead of 1:5. Assign: @ococrook (@broncio123 can do too, but not very familiar with what methods need replacement)

• [x] #40

• [x] Unit tests. Assign: @ococrook

• [x] Use rlog functions in app_v2 module to handle logs more graciously and direct log history to file. Check this. Assing: @broncio123

• [ ] #41

• [ ] Add examples of use in docstrings of streamline backend functions. Assign: @broncio123

• [ ] Find out why colouring is inconsistent between Protection/Deprotection heatmap and PDB viewer. Assign: @broncio123

• [x] Specify parent module for those methods with identical names in other modules. Assign: @broncio123

[broncio123]

@ococrook feel free to edit the list above. I probably forgot I few more we talked about.

[ococrook]

extract_hdx_data fails if there spaces in csv titles, because when R loads them it will replaces spaces with a .. Do we tell people to format their csvs correctly or handle this?

[broncio123]

Yes, sounds sensible to ask users to at least format their titles with underscores. However, I can add a check to spot those cases to raise an error whenever the number of titles and data cols don't match.