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PhanstielLab / plotgardener

https://phanstiellab.github.io/plotgardener/
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Annotate multiple SNPs with rsID on a Manhattan plot #109

Open Knetsy opened 5 months ago

Knetsy commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

Hi Nicole,

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

Best,

Deborah