Rectangular manhattan plot - color the signal with 2 different significance lines

[dianacornejo]

Hello, I wonder if its possible to color the signals above the 2 significance lines in the same way. What I'm seeing is for example those below 3x10-7 they are being color correctly and those below 2.5x10-6 are shown in gray. It is possible to change this behaviour for all off them without caring if they are below -6 or -7 to have the same colors??? This is an example of my manhattan plot. Thank you

[YinLiLin]

You may try to use highlight function.

[EasperOne]

Agreed, just collect the SNPs above the lower line into a factor. I think the alternate color setting here was demonstrated in the README.