Outstanding issues for HDX streamline features

[broncio123]

Loose ends (bugs and potential enhancements)

• Find out why Manhattan plots fail for Case Study No. 3
  

  hdxstats/vignettes/tutorial-streamline.Rmd

  Lines 369 to 372 in db12beb

  	```{r}
  	graphics_kinetics <- visualise_hdx_data(results, type = "kinetics")
  	graphics_forest <- visualise_hdx_data(results, type="forest")
  	```

  
  . Assign: @broncio123

• 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

• 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)

• Replace the use of slots with Accessors, as suggested in Bioconductor guidelines. Assign: @broncio123 #40

• Unit tests. Assign: @ococrook

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

• Replace use of print with rlog functions for baseline hdxstats modules. Assign: @ococrook #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

• 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.