Hi,

I'm using qqman in R to draw a Manhattan plot (not SNPs, but DNA methylation data of 450K Illumina arrays, but this won't make a difference for this particular question).

I can highlight specific CpGs of interest using the highlight = in the manhattan function, however, I would like to change this color green to a different more visible color (like red). I do not find any information on whether I can change this highlight color, only on how to change the colors per chromosome.

This is the code I use:

qqman::manhattan(a, chr = "CHR", bp = "MAPINFO", p = "P.value", snp = "CPG.Labels", main = "Manhattan Plot", chrlabs = c(1:22), suggestiveline = -log10(1e-05), cex = 0.6, cex.axis = 0.9, genomewideline = -log10(5e-08), highlight = b, logp = TRUE)

I'm not a bioinformatician, but need to use R for my analyses, so please excuse me if this is a very obvious question.

Thank you very much for your help and time.

Kind regards,
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