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totajuliusd / topr

topr is a collection of plotting functions for visualizing and exploring genetic association results. Association results from multiple phenotypes can be viewed simultaneously, over the entire genome (Manhattan plot) or in the more detailed regional view.
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'annotate' function #87

Closed MC4R closed 2 months ago

MC4R commented 2 months ago

Hi,

Thank you very much for this wonderful package. I find it very helpful for visualizing GWAS results.

I noticed that the annotate feature only annotates one locus when two signals are very close to each other. Is there a way to label the top variant from each region, irrespective of how close it is to another signal in that region?

Cheers Dev

totajuliusd commented 2 months ago

Hi and thank you. The region_size argument controls the density of the labelling and its set to 10mb by default. Can you obtain what you want by reducing it? For example by doing:

manhattan(CD_UKBB, annotate=1e-15, region_size = 10000)

MC4R commented 2 months ago

Hi,

Thank you. This is very helpful.

I was trying to plot the APOE region on chromosome 19 where there are many signals close to each other and the annotations do not look great in this case. Do you have any thoughts on how to adjust this to avoid overlap? Thank you.

test

Cheers Dev

totajuliusd commented 2 months ago

Yes, you can use the arguments nudge_y and nudge_x to move the labels. If setting just those parameter doesnt suffice, you can do something like this:

top_hits <- topr::CD_UKBB %>% get_lead_snps()
df1 <- top_hits[seq(1, nrow(top_hits), by = 2), ]
df2 <- top_hits[seq(2, nrow(top_hits), by = 2), ]

manhattan(list(CD_UKBB, df1, df2), annotate=c(1e-30, 1e-9, 1e-9), color=rep("darkblue", 3), nudge_x=c(0, -10000000, 10000000), nudge_y=c(0, 2, 1), show_legend=F)

image

MC4R commented 2 months ago

Thank you very much.