Points sometimes don't color correctly

[timwoelfle]

Thanks for the great package! However, I have noticed that the points sometimes don't color correctly: the lead SNP isn't purple but another (random?) SNP is. Also, it would be great if we could accommodate "secondary lead" SNPs that are labelled but not as big as the lead SNP. Currently, when I try multiple lead SNPs, they're labelled correctly but I can't tell which one is the main lead SNP that defines LD. I have reinstalled the package a few days ago:

Packaged: 2019-08-20 13:25:13 UTC;
Built: R 3.5.3; ; 2019-08-20 13:25:14 UTC; windows

Wrong coloring with one lead SNP:

Wrong coloring with multiple lead SNPs:

[boxiangliu]

Hello Tim,

Thank you so much for looking for these bugs - and sorry for the significant delay on my end.

For the first (incorrect coloring of lead SNP), would you be able to send an example file to reproduce your plot? That way I can track exactly which line is buggy. I am guessing it is the get_lead_snp function, but I want to double-check.

For the second, I think this is a useful feature to have. It should be fairly easy too. I will try to implement this in the near future.