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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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Adding tags to significant points in multitrait / multitrack QQ plots #117

Open evatosco opened 5 months ago

evatosco commented 5 months ago

Hi! Thanks for this R package, I think it's precious and very useful.

I have been looking for a way to show SNP names or gene names of significant points (out of the diagonal line or considering a threshold in observed P-values, for example) in multitrait and multitrack QQ plots, just like the package can show gene names or SNP names in Manhattan plots. Unfortunately, I can't do it yet.

The "highlight" options do not cause an error when running the "CMplot qplot" function; it runs correctly, but no text is shown in the QQ plots. I guess the function just omits them when plotting something else than a Manhattan. They do affect the Manhattan plots correctly.

I was wondering if this option exists in the package, and I missed it, or if anyone knows a way to do it. I figured I could try to add the names manually, but I am not by far an R expert and I think that the resulting plots are not recognizable by other packages to manually add a text per point or something similar. If there's any way to do so, I would deeply appreciate some enlightening!

Thanks in advance! Best regards, Eva

YinLiLin commented 5 months ago

Hi, thank you for the feedback. Sorry that the highlight function for SNP names or gene names is now only available to traditional rectangular-Manhattan plot.

evatosco commented 5 months ago

Hi!

No problem! I needed confirmation that I did not miss it but instead, it does not exist for now. Are there any plans to include this option in the future?

Thanks!