Annotate multiple SNPs with rsID on a Manhattan plot

[Knetsy]

Hello,

I successfully plot a Manhattan plot using plotManhattan and was able to annotate the lead SNP with the leadSNP parameter.
I would like to plot multiple SNPs with their rsID and I wanted to know how I can achieve this?

Thank you very much.

Best,

Deborah

[nekramer]

Hi Deborah,

Unfortunately this feature is out of scope for the current version of plotgardener. However, I have started working on an experimental feature to annotate multiple SNPs in a Manhattan plot in the branch "plotManhattan_features". In this branch, plotManhattan now has a snpHighlights parameter instead of the leadSNP parameter and this takes a data.frame where you can specify multiple SNPs and corresponding aesthetics. For example, if you had "rs1" and "rs2" and wanted to make one a blue diamond and the other a green diamond, you would specify snpHighlights = data.frame("snp" = c("rs1", "rs2"), pch = c(23, 23), fill = c("blue", "green")). However, because this is experimental and not completely developed yet, I don't yet have any functionality for labeling the rsIDs of the multiple SNPs. The best way to overcome this would be to use plotText on top of the Manhattan plot, but I know this isn't an ideal solution.

If you are still interested in trying out the experimental feature (or even contributing to it), you can grab the plotManhattan_features branch:
devtools::install_github("PhanstielLab/plotgardener", ref = "plotManhattan_features")

Best,
Nicole

[Knetsy]

Hi Nicole,

Thank you very much! I will try the experimental feature in a near future :)

Best,

Deborah