How to highlight genes on a Manhattan plot
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8.5 years ago
kyoko777 • 0

Hi. I've been looking for a way to make a Manhattan plot with highlights for the genes on interest like this.

< image missing >

Is there any software to draw this?

If not (or it's very expensive), how can I make this using R? I am using qqman.r. What I wish to do is highlight different sets of SNPs in different colors.

I looked at another post similar to my question, but I am looking for a way to highlight arbitrary genes in different colors instead of genes below thresholds although the example I attached shows the latter ones.

Thank you in advance!

(I edited my question to make it clear.)

R gene SNP • 7.8k views
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Well, the general idea is to just change the color of that gene (and possibly those neighboring it). Do you know how to specify colors in R or do you need help with that as well?

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Thank you for your help. I use qqman.r and basically follow the instruction on this site. If I can highlight multiple genes in different colors with annotations, that would be wonderful. I just started learning how to draw graphs using R, so your help for coloring is much appreciated!

Meanwhile, I am still wondering if there is a software or code for the example plot because I've seen the same style in different papers. They might be made by the same group of authors..

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The qqman package allows you to highlight specific positions, note the annotate= option to the manhattan() function. You can just pass a list of SNPs/genes to it. I don't know if there's an option to add labels within that package, but if not I'm sure it's possible to tweak the functions if you learn how to code in R.

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Thank you very much! I actually have done the highlight= option (annotate= option actually add rs#, so I guess it's a mistake). What I wish to do is to highlight several groups of SNPs in different colors, for which I don't know how to tweak. Maybe I can add a highlight2= option for another set in a different color?

I read in another post that you can just add text for gene names.

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I'm not familiar enough with qqman to say. If you know how to program in R then you should be able to simply modify the manhattan() function.

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Unfortunately, I don't know how to program in R very much yet, but I will post the code if I manage to do it. Thank you very much anyway!

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You might give this post another day to see if someone familiar with that package replies. If not, I'd recommend posting to the R-help email list and mentioning what you're trying to do with the qqman package and see if there's anything obvious (or not so obvious) that you've missed that would allow you to do that. You'll need to CC the qqman maintainer in the email and hopefully Stephen (the maintainer of that package) would add this as a new feature if there's no current good way to do it.

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Thank you very much for your advice! R-help sounds like a better place to ask a question like this.

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Hi, have you figure out how to color the different SNPs group in different colors? Thanks!

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