Miscellaneous improvements to ctwas

[pcarbo]

@kevinlkx I'm going to use this issue to document some miscellaneous suggested improvements to the package. I will continue to add items here as I review the package. (Note: make these improvements to the "multigroup_test" branch.)

• [x] Add a CITATION file. See here for an example.

• [x] Replace @import statements with @importFrom statements. (Importing all the functions in a package seems risky; I would advise against it.)

• [x] Fix non-portable file names (I think the issue is the colon in these file names):

  inst/extdata/sample_data/cor_matrix/region.16:71020125-72901251.R_gene.RDS
  inst/extdata/sample_data/cor_matrix/region.16:71020125-72901251.R_snp_gene.RDS
  inst/extdata/sample_data/cor_matrix/region.16:71020125-72901251.R_snp.RDS

• [ ] Make sure all arguments to merge_finemap_regions() are documented. Currently, "LD_format" and "LD_loader_fun" are not documented.

• [ ] It would be helpful if make_convergence_plots() had a single parameter controlling the overall font size; right now when I create the plots, the text for the axes is quite large. For example when I use theme_cowplot() this is quite easy since it has a "font_size" argument. The same comment applies to other plotting functions such as make_locusplot().

• [ ] For the locus zoom plot, it is hard to distinguish squares from circles when there are overplotted. Can the color and shape be changed? Also, looks like you are varying size as well, but this does not show up in the legend. Also, there is no explanation in the legend what "red" represents.

[kevinlkx]

@pcarbo I added a CITATION file. Do we need to add a link to this CITATION file?

[pcarbo]

No, you run this in R to get the citation:

citation("ctwas")

[pcarbo]

Feel free to check the items in the list if they are completed.

[pcarbo]

Added a couple items.