Ts add vignettes

[TomSmithCGAT]

@csdaw - Would you mind taking a look at the SILAC vignette. If you have longer comments you don't want to add here, happy to talk in person

[csdaw]

Going through code and text now. Just a first thing, am I okay to remove objects that are created but never used? e.g. https://github.com/CambridgeCentreForProteomics/camprotR/blob/cec8e67f8dda8ab890a142dd47d8916854be8c6e/vignettes/SILAC.Rmd#L224-L231

[TomSmithCGAT]

Why would you want to do that? Random objects help to force the reader to work through it all properly and identify where the inefficiencies are 😜

[csdaw]

By that logic we should put an error at the very end, and the reader has only understood if they can fix it!

[TomSmithCGAT]

Don't tempt me..

[csdaw]

I've made lots of very pedantic small changes but nothing major like adding or removing content. It reads well and I think its fine as is (although will probably get feedback once someone who is not you or me works through the vignette).

I've done the following to the code:

• Add explicit calls to library() for each dependency so its obvious what is needed to run the vignette. This is perhaps not 'recommended' if you're only using a single function from an entire massive library e.g. Biostrings but I think it will help the people actually using the vignette.
• Reordered the loading of dependencies so one doesn't overwrite functions from dplyr, so you don't need to use dplyr::select for example
• Wrap code to roughly 80 char and small changes to 'style'
• Make ggplot layer ordering consistent throughout
• Make what is being plotting to x and y axes explicit
• Change some of the dplyr/tidyr/tibble code chunks to what I think of as 'best practice'

And the following to the text:

• Adjust the title slightly
• Add section titles
• Make language around SILAC experiment background a bit more clear
• Fixed a couple of typos

[TomSmithCGAT]

All looks good to me. @csdaw, you happy if I squash and merge?

[csdaw]

@TomSmithCGAT Go for it!